X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PKYPDB ENTRY 1PKY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.86% PEG 4000, 20MM AMMONIUM SULPHATE, 15% GLYCEROL, 20MM SODIUM ACETATE PH 4.8
Crystal Properties
Matthews coefficientSolvent content
3.3362.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.649α = 90
b = 132.638β = 97.11
c = 180.996γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHBENT FUSED QUARTZ SINGLE SEGMENT MIRROR1997-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX7.2SRSPX7.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.3530680.0895.41.5160789
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.4847.40.3082.41.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONOTHERTHROUGHOUTPDB ENTRY 1PKY2.3530160789807467.90.2090.2090.256RANDOM48.9
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]
-12.518-4.150911.19941.3186
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d24
x_angle_deg1.4
x_improper_angle_d1.2
x_bond_d0.009
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d24
x_angle_deg1.4
x_improper_angle_d1.2
x_bond_d0.009
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
x_mcbond_it
x_mcangle_it
x_scbond_it
x_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms29994
Nucleic Acid Atoms
Solvent Atoms2952
Heterogen Atoms40

Software

Software
Software NamePurpose
AMoREphasing
FFTmodel building
SHELXSphasing
MLPHAREphasing
DMmodel building
X-PLORrefinement
DENZOdata reduction
CCP4data scaling
FFTphasing
DMphasing