3TOH

HIV-1 Protease - Epoxydic Inhibitor Complex (pH 9 - Orthorombic Crystal form P212121)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NMZPDB ENTRY 2NMZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9298Ammonium sulfate 40%, DMSO 10%, sodium citrate 0.25M. pH has been increased through ammonia diffusion, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1442.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.268α = 90
b = 58.377β = 90
c = 61.3γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMIRRORS2008-06-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R1.0ELETTRA5.2R

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
11.11642.2695.70.04710.52.7578906973122
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)
11.1161.1783.70.3912.92.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 2NMZ1.11642.26266936279696.770.178220.176830.21139RANDOM12.477
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]
-0.520.080.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.552
r_dihedral_angle_4_deg19.082
r_dihedral_angle_3_deg12.496
r_dihedral_angle_1_deg6.004
r_sphericity_free5.956
r_scangle_it4.46
r_sphericity_bonded3.834
r_scbond_it3.016
r_mcangle_it2.181
r_mcbond_it1.588
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.552
r_dihedral_angle_4_deg19.082
r_dihedral_angle_3_deg12.496
r_dihedral_angle_1_deg6.004
r_sphericity_free5.956
r_scangle_it4.46
r_sphericity_bonded3.834
r_scbond_it3.016
r_mcangle_it2.181
r_mcbond_it1.588
r_rigid_bond_restr1.587
r_angle_refined_deg1.486
r_symmetry_hbond_refined0.349
r_nbtor_refined0.313
r_symmetry_vdw_refined0.203
r_nbd_refined0.196
r_xyhbond_nbd_refined0.157
r_chiral_restr0.095
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1512
Nucleic Acid Atoms
Solvent Atoms183
Heterogen Atoms51

Software

Software
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling