2BO9

Human carboxypeptidase A4 in complex with human latexin.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherCPA4 WITHIN PCPA4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.540% MPD; 0.1M BIS-TRIS PH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.957

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.922α = 90
b = 96.651β = 99.6
c = 92.358γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.648.399.80.0711.83.817940113.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6999.30.264.83.7

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTCPA4 WITHIN PCPA41.65017870667899.80.150.1490.176RANDOM17.28
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]
1.98-0.24-1.36-0.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.361
r_dihedral_angle_4_deg16.368
r_dihedral_angle_3_deg13.03
r_dihedral_angle_1_deg6.187
r_scangle_it3.357
r_scbond_it2.126
r_angle_refined_deg1.348
r_mcangle_it1.343
r_mcbond_it0.884
r_nbd_refined0.207
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.361
r_dihedral_angle_4_deg16.368
r_dihedral_angle_3_deg13.03
r_dihedral_angle_1_deg6.187
r_scangle_it3.357
r_scbond_it2.126
r_angle_refined_deg1.348
r_mcangle_it1.343
r_mcbond_it0.884
r_nbd_refined0.207
r_symmetry_vdw_refined0.15
r_xyhbond_nbd_refined0.125
r_symmetry_hbond_refined0.106
r_chiral_restr0.097
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8404
Nucleic Acid Atoms
Solvent Atoms1153
Heterogen Atoms146

Software

Software
Software NamePurpose
DMmodel building
SCALAdata scaling
AMoREphasing
MLPHAREphasing
SIGMAAphasing
DMphasing
REFMACrefinement