X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DRYPDB Entry 1DRY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62912.5 M sodium acetate, 0.1 M Hepes, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.8260.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.61α = 90
b = 91.61β = 90
c = 90.878γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2006-06-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X13EMBL/DESY, HAMBURGX13

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
11.452399.70.0612.63.85780000.921
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)
11.451.5399.70.9920.93.9911338

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB Entry 1DRY1.4522.9177685234299.640.1710.170.186RANDOM18.473
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]
0.210.10.21-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.837
r_dihedral_angle_4_deg18.792
r_dihedral_angle_3_deg10.898
r_dihedral_angle_1_deg5.415
r_scangle_it2.675
r_scbond_it1.742
r_angle_refined_deg1.175
r_mcangle_it0.954
r_angle_other_deg0.9
r_mcbond_it0.856
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.837
r_dihedral_angle_4_deg18.792
r_dihedral_angle_3_deg10.898
r_dihedral_angle_1_deg5.415
r_scangle_it2.675
r_scbond_it1.742
r_angle_refined_deg1.175
r_mcangle_it0.954
r_angle_other_deg0.9
r_mcbond_it0.856
r_symmetry_vdw_other0.346
r_symmetry_hbond_refined0.213
r_nbd_refined0.211
r_nbd_other0.206
r_nbtor_refined0.168
r_xyhbond_nbd_refined0.148
r_symmetry_vdw_refined0.136
r_mcbond_other0.128
r_nbtor_other0.083
r_chiral_restr0.065
r_metal_ion_refined0.034
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2418
Nucleic Acid Atoms
Solvent Atoms342
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing