2NXL

Structure of HIV-1 protease D25N complexed with the rt-rh analogue peptide GLY-ALA-GLU-VAL-PHE*TYR-VAL-ASP-GLY-ALA


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 pH 6.2; 63mM sodium citrate; 25-35% Ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.86 α = 90
b = 57.5 β = 90
c = 61.89 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 Yale mirrors 2005-03-11
Diffraction Radiation
Monochromator Protocol
Yale 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
2 42.11 95.8 0.071 0.071 -- 5.0 12332 12332 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 2.0 42.11 -- 0.0 11693 11693 608 95.92 0.16307 0.16307 0.16035 0.216 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 2.0 2.049 -- 39 794 0.181 0.251 -- 89.09
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 37.719
Anisotropic B[1][1] 1.08
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.09
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 12.352
r_nbd_other 0.184
r_nbtor_refined 0.17
r_dihedral_angle_2_deg 39.41
r_nbd_refined 0.198
r_mcbond_other 0.152
r_dihedral_angle_1_deg 6.659
r_angle_refined_deg 1.455
r_symmetry_vdw_refined 0.169
r_gen_planes_refined 0.005
r_scangle_it 2.1
r_chiral_restr 0.087
r_xyhbond_nbd_refined 0.133
r_gen_planes_other 0.001
r_symmetry_vdw_other 0.206
r_bond_refined_d 0.007
r_mcangle_it 0.897
r_symmetry_hbond_refined 0.16
r_scbond_it 1.411
r_bond_other_d 0.001
r_angle_other_deg 0.781
r_symmetry_hbond_other 0.05
r_mcbond_it 0.723
r_dihedral_angle_3_deg 13.77
r_nbtor_other 0.084
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1565
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 137

Software

Software
Software Name Purpose
AMoRE phasing
REFMAC refinement version: 5.2
DENZO data reduction
SCALEPACK data scaling