2B9E | pdb_00002b9e

Human NSUN5 protein


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IXK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5300NSUN5 was complexed with S-adenosyl-L-methionine (SAM) (Sigma) at 1:10 molar ratio of protein :SAM and crystallized using the sitting drop vapor diffusion method at 20 C by mixing 1 l of the protein solution with 1 l of the reservoir solution containing 10% Iso-propanole, 20% PEG 4000, 0.1M Na HEPES pH 7.5. , VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.347

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.289α = 90
b = 56.289β = 90
c = 178.666γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2005-10-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.6559.5599.753841538415
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.651.69390

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1IXK1.6559.553841538415203899.750.188070.186240.190.222260.18RANDOM22.801
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]
0.830.420.83-1.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.119
r_dihedral_angle_4_deg22.224
r_dihedral_angle_3_deg12.073
r_dihedral_angle_1_deg6.529
r_scangle_it3.314
r_scbond_it2.135
r_mcangle_it1.571
r_angle_refined_deg1.326
r_mcbond_it0.913
r_nbtor_refined0.307
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2127
Nucleic Acid Atoms
Solvent Atoms432
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing