3TOF

HIV-1 Protease - Epoxydic Inhibitor Complex (pH 6 - 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 DROP6298Ammonium sulfate 40%, DMSO 10%, sodium citrate 0.25M, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1342.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.294α = 90
b = 58.392β = 90
c = 61.026γ = 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 5.2R1.2ELETTRA5.2R

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
11.4513.5696.10.07310.43.53184922
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)
11.451.576.40.04561.92.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 2NMZ1.4513.5623284430233161796.20.20340.187220.184120.24574RANDOM14.163
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]
-0.050.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.342
r_dihedral_angle_4_deg21.715
r_dihedral_angle_3_deg13.79
r_sphericity_free8.489
r_scangle_it6.056
r_dihedral_angle_1_deg5.976
r_sphericity_bonded4.592
r_scbond_it4.325
r_mcangle_it3.022
r_rigid_bond_restr2.501
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.342
r_dihedral_angle_4_deg21.715
r_dihedral_angle_3_deg13.79
r_sphericity_free8.489
r_scangle_it6.056
r_dihedral_angle_1_deg5.976
r_sphericity_bonded4.592
r_scbond_it4.325
r_mcangle_it3.022
r_rigid_bond_restr2.501
r_mcbond_it2.388
r_angle_refined_deg1.967
r_symmetry_hbond_refined0.352
r_nbtor_refined0.317
r_symmetry_vdw_refined0.222
r_nbd_refined0.214
r_chiral_restr0.144
r_xyhbond_nbd_refined0.13
r_bond_refined_d0.023
r_gen_planes_refined0.01
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 Atoms177
Heterogen Atoms54

Software

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