X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52930.1M Na citrate pH 5.0, 30% PEG 550MME, 0.2M NaSCN
Crystal Properties
Matthews coefficientSolvent content
1.9737.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.843α = 90
b = 44.843β = 90
c = 158.235γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2019-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.5850990.0510.0540.0211.47.642279
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.581.6497.90.4690.5040.1830.8937.4

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 REPLACEMENTTHROUGHOUT1QWD1.5831.7340941131799.090.16440.16320.2025RANDOM20.032
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]
-0.59-0.591.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.261
r_dihedral_angle_4_deg18.317
r_dihedral_angle_3_deg14.329
r_dihedral_angle_1_deg6.718
r_angle_refined_deg2.394
r_angle_other_deg0.973
r_chiral_restr0.211
r_bond_refined_d0.023
r_gen_planes_refined0.013
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.261
r_dihedral_angle_4_deg18.317
r_dihedral_angle_3_deg14.329
r_dihedral_angle_1_deg6.718
r_angle_refined_deg2.394
r_angle_other_deg0.973
r_chiral_restr0.211
r_bond_refined_d0.023
r_gen_planes_refined0.013
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2558
Nucleic Acid Atoms
Solvent Atoms231
Heterogen Atoms109

Software

Software
Software NamePurpose
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection
HKL-2000data reduction