7PRB

Crystal structure of Burkholderia pseudomallei heparanase in complex with covalent inhibitor GR109


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5BWI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52930.1 M sodium citrate pH 5.0, 14% (w/v) PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.6152.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.21α = 90
b = 101.07β = 90
c = 113.59γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2019-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97933DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim 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
11.3166.0698.50.0510.0180.99915.78.3220199
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.311.341.4930.5340.6821.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5bwi1.3166.062201061104398.3610.1670.16570.185522.799
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]
1.858-0.637-1.221
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.701
r_dihedral_angle_4_deg12.568
r_dihedral_angle_3_deg12.133
r_dihedral_angle_1_deg6.809
r_lrange_it5.616
r_lrange_other5.342
r_scangle_it4.305
r_scangle_other4.304
r_scbond_it2.878
r_scbond_other2.877
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.701
r_dihedral_angle_4_deg12.568
r_dihedral_angle_3_deg12.133
r_dihedral_angle_1_deg6.809
r_lrange_it5.616
r_lrange_other5.342
r_scangle_it4.305
r_scangle_other4.304
r_scbond_it2.878
r_scbond_other2.877
r_mcangle_other2.484
r_mcangle_it2.481
r_angle_refined_deg1.897
r_mcbond_it1.811
r_mcbond_other1.802
r_angle_other_deg1.607
r_nbd_other0.326
r_chiral_restr0.293
r_symmetry_nbd_refined0.283
r_symmetry_xyhbond_nbd_refined0.254
r_nbd_refined0.233
r_xyhbond_nbd_refined0.21
r_symmetry_nbd_other0.175
r_nbtor_refined0.173
r_symmetry_xyhbond_nbd_other0.11
r_symmetry_nbtor_other0.086
r_ncsr_local_group_10.086
r_xyhbond_nbd_other0.079
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_gen_planes_other0.006
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6291
Nucleic Acid Atoms
Solvent Atoms991
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
REFMACphasing