X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QGVPDB ENTRY 1QGV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
12951.4 M NaCl, pH 9.0, VAPOR DIFFUSION, temperature 295 K
Crystal Properties
Matthews coefficientSolvent content
2.653.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.877α = 90
b = 109.877β = 90
c = 85.17γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-08-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-BMAPS17-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.7341.595.40.0610.06111.32.92082020820
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.731.8691.30.3850.3852.282.5

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1QGV1.7341.5199501989566698.770.209580.207980.26115RANDOM20.552
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]
-0.17-0.08-0.170.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.611
r_dihedral_angle_4_deg25.447
r_dihedral_angle_3_deg13.695
r_dihedral_angle_1_deg6.256
r_scangle_it4.308
r_scbond_it2.753
r_mcangle_it1.735
r_angle_refined_deg1.459
r_mcbond_it1.217
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.611
r_dihedral_angle_4_deg25.447
r_dihedral_angle_3_deg13.695
r_dihedral_angle_1_deg6.256
r_scangle_it4.308
r_scbond_it2.753
r_mcangle_it1.735
r_angle_refined_deg1.459
r_mcbond_it1.217
r_nbtor_refined0.303
r_symmetry_vdw_refined0.228
r_nbd_refined0.199
r_xyhbond_nbd_refined0.171
r_symmetry_hbond_refined0.168
r_chiral_restr0.114
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1115
Nucleic Acid Atoms
Solvent Atoms199
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
MOLREPphasing
ARP/wARPmodel building