4EJD

HIV Protease (PR) dimer in closed form with pepstatin in active site and fragment 1F1 in the outside/top of flap


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.52980.2 M potassium bromide, 0.2 M potassium thiocyanate, 3% PGA-LM, 3% MPD, 10% DMSO, 0.1 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9737.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 28.82α = 90
b = 65.63β = 90
c = 92.93γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rRh coated flat mirror2010-06-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-10.979SSRLBL7-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.10392.9398.30.0898.33.47060970609
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.1031.1699.90.4830.4831.53.310342

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.10318.9670371354397.770.14750.14590.1762RANDOM14.7297
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]
-0.02-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.956
r_sphericity_free35.424
r_dihedral_angle_3_deg14.202
r_dihedral_angle_4_deg11.903
r_sphericity_bonded10.978
r_rigid_bond_restr10.33
r_dihedral_angle_1_deg6.865
r_angle_other_deg2.064
r_angle_refined_deg1.442
r_chiral_restr0.139
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.956
r_sphericity_free35.424
r_dihedral_angle_3_deg14.202
r_dihedral_angle_4_deg11.903
r_sphericity_bonded10.978
r_rigid_bond_restr10.33
r_dihedral_angle_1_deg6.865
r_angle_other_deg2.064
r_angle_refined_deg1.442
r_chiral_restr0.139
r_gen_planes_refined0.015
r_bond_refined_d0.01
r_gen_planes_other0.002
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1562
Nucleic Acid Atoms
Solvent Atoms165
Heterogen Atoms30

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection