Experiment: 3QKD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YXJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	1.1M Sodium Citrate, 0.1M Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.598	α = 90
b = 74.484	β = 90
c = 87.828	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	IMAGE PLATE	RIGAKU RAXIS IV++	Capillary	2007-03-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.02	50	96.45	0.072	22.9	6.2	28962	27934	-3	-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.02	2.09	55.8		0.499	3.15		2525

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2YXJ	2.02	43.9	27379	26408	1450	96.45	0.19384	0.19384	0.19184	0.23093	RANDOM	28.758

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.59			1.68		-1.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.532
r_dihedral_angle_4_deg	16.838
r_dihedral_angle_3_deg	15.603
r_dihedral_angle_1_deg	5
r_scangle_it	2.391
r_scbond_it	1.461
r_angle_refined_deg	1.152
r_mcangle_it	1.078
r_mcbond_it	0.62
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.532
r_dihedral_angle_4_deg	16.838
r_dihedral_angle_3_deg	15.603
r_dihedral_angle_1_deg	5
r_scangle_it	2.391
r_scbond_it	1.461
r_angle_refined_deg	1.152
r_mcangle_it	1.078
r_mcbond_it	0.62
r_nbtor_refined	0.308
r_nbd_refined	0.186
r_symmetry_vdw_refined	0.168
r_xyhbond_nbd_refined	0.167
r_symmetry_hbond_refined	0.142
r_chiral_restr	0.077
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2293
Nucleic Acid Atoms
Solvent Atoms	210
Heterogen Atoms	123

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.