9DQA | pdb_00009dqa

Crystal structure of bovine RPE65 in complex with EYE-002


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4RSC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5281100 mM Tris-HCl pH 8.5, 30% PEG 200, 200 mM ammonium phosphate
Crystal Properties
Matthews coefficientSolvent content
3.1661.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 175.81α = 90
b = 175.81β = 90
c = 86.46γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2024-05-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.979460SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.15098.80.1530.9978.51087750
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.222.0250.2980.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.147.90687750449798.770.1820.18010.1870.20890.214146.496
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]
0.8280.4140.828-2.687
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg12.373
r_dihedral_angle_3_deg9.511
r_lrange_it6.841
r_lrange_other6.84
r_dihedral_angle_1_deg6.806
r_dihedral_angle_2_deg3.992
r_scangle_it3.581
r_scangle_other3.581
r_mcangle_other3.245
r_mcangle_it3.244
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg12.373
r_dihedral_angle_3_deg9.511
r_lrange_it6.841
r_lrange_other6.84
r_dihedral_angle_1_deg6.806
r_dihedral_angle_2_deg3.992
r_scangle_it3.581
r_scangle_other3.581
r_mcangle_other3.245
r_mcangle_it3.244
r_scbond_it2.086
r_scbond_other2.086
r_mcbond_it1.9
r_mcbond_other1.898
r_angle_refined_deg0.914
r_angle_other_deg0.334
r_symmetry_nbd_other0.175
r_nbtor_refined0.175
r_nbd_refined0.171
r_nbd_other0.162
r_symmetry_xyhbond_nbd_refined0.159
r_symmetry_nbd_refined0.148
r_xyhbond_nbd_refined0.124
r_metal_ion_refined0.096
r_symmetry_nbtor_other0.078
r_ncsr_local_group_10.056
r_chiral_restr0.047
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8153
Nucleic Acid Atoms
Solvent Atoms987
Heterogen Atoms76

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing