X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YWVAPO Structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5277Na Acetate, Imidazole, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.867

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.315α = 90
b = 99.315β = 90
c = 80.561γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-07-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.1ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.284.5199.8230051.51.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.26100

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUTAPO Structure2.284.511.52300521771117899.770.197240.195080.23668RANDOM27.464
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]
1.490.741.49-2.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg2.941
r_scangle_it2.584
r_scbond_it1.531
r_angle_refined_deg1.385
r_mcangle_it1.089
r_angle_other_deg0.906
r_mcbond_it0.575
r_symmetry_vdw_other0.297
r_nbd_other0.237
r_nbd_refined0.197
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg2.941
r_scangle_it2.584
r_scbond_it1.531
r_angle_refined_deg1.385
r_mcangle_it1.089
r_angle_other_deg0.906
r_mcbond_it0.575
r_symmetry_vdw_other0.297
r_nbd_other0.237
r_nbd_refined0.197
r_symmetry_vdw_refined0.182
r_xyhbond_nbd_refined0.179
r_symmetry_hbond_refined0.158
r_chiral_restr0.093
r_nbtor_other0.082
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2231
Nucleic Acid Atoms
Solvent Atoms174
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing