2H3L | pdb_00002h3l

Crystal Structure of ERBIN PDZ


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MFGPDB Entry: 1MFG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.52920.1 M TRIS-HCL, 35% PEG 4000, pH 7.5-8.5, vapor diffusion, temperature 292K, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
2.141.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.864α = 90
b = 44.032β = 106.18
c = 57.265γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2002-05-02MSINGLE WAVELENGTH
21x-rayM
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-2SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (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
1,213099.40.07119.53.2100042
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.0497.60.5171.62.7

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 (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB Entry: 1MFG13010021894642471194.40.148720.1480.160.1690.18RANDOM12.9
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]
-0.19-0.040.110.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.207
r_dihedral_angle_4_deg17.297
r_sphericity_free15.068
r_dihedral_angle_3_deg9.963
r_sphericity_bonded6.659
r_dihedral_angle_1_deg6.32
r_scangle_it5.998
r_mcangle_it4.365
r_scbond_it4.239
r_mcbond_it3.707
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1543
Nucleic Acid Atoms
Solvent Atoms268
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
AMoREphasing