2QI3

Crystal structure of protease inhibitor, MIT-2-AD94 in complex with wild type HIV-1 protease


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 298.0
Details 126 mM Sodium Phosphate, 63 mM sodium citrate, 24-29% ammonium sulphate , pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.88 α = 90
b = 58.37 β = 90
c = 61.84 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 200
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV osmic mirrors 2006-08-22
Diffraction Radiation
Monochromator Protocol
osmic mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.5418 -- --

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.95 50 98.2 0.066 6.6 -- 6.9 -- 13691 0.0 0.0 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.95 42.45 0.0 0.0 12976 12976 683 98.22 0.17552 0.17552 0.17363 0.21045 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.95 2.002 -- 50 890 0.203 0.272 -- 94.95
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.813
Anisotropic B[1][1] -0.99
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.32
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.31
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.001
r_dihedral_angle_4_deg 17.087
r_xyhbond_nbd_refined 0.112
r_mcangle_it 0.658
r_nbtor_other 0.079
r_scangle_it 1.417
r_symmetry_vdw_other 0.166
r_symmetry_hbond_refined 0.14
r_angle_refined_deg 1.16
r_gen_planes_refined 0.003
r_symmetry_vdw_refined 0.132
r_dihedral_angle_1_deg 6.042
r_nbd_refined 0.178
r_angle_other_deg 0.694
r_mcbond_other 0.087
r_scbond_it 0.895
r_nbtor_refined 0.166
r_gen_planes_other 0.001
r_dihedral_angle_3_deg 10.213
r_dihedral_angle_2_deg 42.791
r_chiral_restr 0.071
r_mcbond_it 0.422
r_bond_refined_d 0.008
r_nbd_other 0.172
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1477
Nucleic Acid Atoms 0
Heterogen Atoms 47
Solvent Atoms 119

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
HKL-2000 data reduction
SCALEPACK data scaling
AMoRE phasing