2PBK

Crystal structure of KSHV protease in complex with hexapeptide phosphonate inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FL1PDB Entry 1FL1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82930.8M NaFormate, 0.1M NaAcetate, 5% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.5651.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.883α = 90
b = 108.941β = 103.71
c = 54.051γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.0ALS8.3.1

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
11.732093.920.04813.24.65093247867
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)
11.7361.750.2054.8

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 REPLACEMENTTHROUGHOUTPDB Entry 1FL11.7319.5747865256893.920.163440.161220.20394RANDOM25.575
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]
0.060.030.04-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.819
r_dihedral_angle_4_deg17.332
r_dihedral_angle_3_deg12.128
r_dihedral_angle_1_deg5.883
r_scangle_it3.535
r_scbond_it2.362
r_mcangle_it1.639
r_angle_refined_deg1.485
r_mcbond_it1.085
r_angle_other_deg0.816
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.819
r_dihedral_angle_4_deg17.332
r_dihedral_angle_3_deg12.128
r_dihedral_angle_1_deg5.883
r_scangle_it3.535
r_scbond_it2.362
r_mcangle_it1.639
r_angle_refined_deg1.485
r_mcbond_it1.085
r_angle_other_deg0.816
r_mcbond_other0.273
r_symmetry_vdw_other0.246
r_nbd_refined0.235
r_symmetry_vdw_refined0.196
r_xyhbond_nbd_refined0.193
r_nbd_other0.183
r_nbtor_refined0.176
r_symmetry_hbond_refined0.158
r_chiral_restr0.149
r_nbtor_other0.084
r_xyhbond_nbd_other0.052
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3613
Nucleic Acid Atoms
Solvent Atoms530
Heterogen Atoms12

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling