3KVC

Crystal structure of bovine RPE65 at 1.9 angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FSNPDB ENTRY 3FSN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP628130% PEG 200 AS PRECIPITANT , pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties
Matthews coefficientSolvent content
3.1961.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 176.356α = 90
b = 176.356β = 90
c = 86.715γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDSI(111) DOUBLE CRYSTAL MONOCHROMETER. ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY2008-11-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.03324APS23-ID-D

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
11.9100990.1040.10417.54.7119836119836-323.234
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)
1.91.97920.5650.5652.263.211075

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 3FSN1.920113526613998.870.147580.146330.17062RANDOM23.369
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]
3.683.68-7.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.809
r_dihedral_angle_4_deg13.944
r_dihedral_angle_3_deg11.831
r_dihedral_angle_1_deg6.726
r_scangle_it3.767
r_scbond_it2.382
r_mcangle_it1.646
r_angle_refined_deg1.455
r_mcbond_it0.943
r_angle_other_deg0.885
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.809
r_dihedral_angle_4_deg13.944
r_dihedral_angle_3_deg11.831
r_dihedral_angle_1_deg6.726
r_scangle_it3.767
r_scbond_it2.382
r_mcangle_it1.646
r_angle_refined_deg1.455
r_mcbond_it0.943
r_angle_other_deg0.885
r_mcbond_other0.254
r_chiral_restr0.093
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8010
Nucleic Acid Atoms
Solvent Atoms503
Heterogen Atoms2

Software

Software
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling