X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17pH 7.0
Crystal Properties
Matthews coefficientSolvent content
3.1761.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.747α = 90
b = 121.747β = 90
c = 68.929γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 1MIRRORS1997-06-09M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE A1CHESSA1

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
12.21597.30.03927.53.625367-328.9
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)
2.22.396.10.10313.13.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1GDD2.215125703244997.30.2270.2270.268TO PREVENT MODEL BIAS, THE SAME TEST REFLECTIONS USED IN THE REFINEMENT OF THE STARTING MODEL (1GDD) WERE USED IN THIS REFINEMENT26.6
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]
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d23.05
x_scangle_it6.62
x_scbond_it4.93
x_mcangle_it4.5
x_mcbond_it3.39
x_angle_deg1.417
x_improper_angle_d1.275
x_bond_d0.01
x_bond_d_na
x_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d23.05
x_scangle_it6.62
x_scbond_it4.93
x_mcangle_it4.5
x_mcbond_it3.39
x_angle_deg1.417
x_improper_angle_d1.275
x_bond_d0.01
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2589
Nucleic Acid Atoms
Solvent Atoms49
Heterogen Atoms39

Software

Software
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing