8RLO | pdb_00008rlo

Human Carbonic Anhydrase I in complex with veralipride


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JV0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP929628-31% PEG4000, 0.2 M sodium acetate, 0.1 M Tris pH 9.0
Crystal Properties
Matthews coefficientSolvent content
2.3647.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.14α = 90
b = 71.25β = 90
c = 121.16γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-11-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C0.97170ELETTRA11.2C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.5546.1999.90.080.0840.99916.0312.480418
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.591001.3861.3380.8512.2112.7

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 DIFFRACTIONMOLECULAR REPLACEMENTNONE1.5546.1980418409599.9380.1710.16860.18590.21820.23629.202
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]
-3.7487.125-3.378
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.236
r_dihedral_angle_4_deg16.886
r_dihedral_angle_3_deg14.057
r_rigid_bond_restr13.557
r_dihedral_angle_1_deg7.876
r_scangle_it6.981
r_scangle_other6.98
r_lrange_it6.687
r_lrange_other6.686
r_scbond_other6.167
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.236
r_dihedral_angle_4_deg16.886
r_dihedral_angle_3_deg14.057
r_rigid_bond_restr13.557
r_dihedral_angle_1_deg7.876
r_scangle_it6.981
r_scangle_other6.98
r_lrange_it6.687
r_lrange_other6.686
r_scbond_other6.167
r_scbond_it6.166
r_mcangle_it5.834
r_mcangle_other5.825
r_mcbond_other5.238
r_mcbond_it5.237
r_angle_refined_deg1.817
r_angle_other_deg1.481
r_nbd_other0.238
r_symmetry_xyhbond_nbd_refined0.219
r_nbd_refined0.213
r_symmetry_nbd_other0.202
r_symmetry_nbd_refined0.173
r_nbtor_refined0.169
r_xyhbond_nbd_refined0.146
r_metal_ion_refined0.119
r_chiral_restr0.1
r_symmetry_nbtor_other0.079
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_bond_other_d0.007
r_gen_planes_other0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4016
Nucleic Acid Atoms
Solvent Atoms296
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing