4DGA

TRIMCyp cyclophilin domain from Macaca mulatta: HIV-1 CA(O-loop) complex


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 290.0
Details 20% w/v PEG5000 MME, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 38.59 α = 90
b = 111.35 β = 102.39
c = 67.76 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2010-04-24
Diffraction Radiation
Monochromator Protocol
single crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 1.0720 ESRF ID23-1

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
1.9 66.18 95.1 -- 0.053 -- 1.8 41766 41766 -- -- 20.45
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.9 2.0 83.1 0.196 0.196 3.6 1.7 5322

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 1.9 66.18 -- 0.0 -- 41697 2111 94.79 -- 0.1983 0.1959 0.2431 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 1.9 1.949 -- 116 2261 0.259 0.339 -- 73.77
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.0759
Anisotropic B[1][1] -0.12
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.21
Anisotropic B[2][2] 1.3
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.27
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.204
r_bond_refined_d 0.008
r_dihedral_angle_2_deg 37.232
r_gen_planes_refined 0.006
r_bond_other_d 0.001
r_dihedral_angle_1_deg 5.785
r_angle_other_deg 0.838
r_dihedral_angle_4_deg 18.734
r_dihedral_angle_3_deg 13.096
r_chiral_restr 0.069
r_gen_planes_other 0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4554
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 349

Software

Software
Software Name Purpose
SCALA data scaling version: 3.3.16
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10
PXSOFT data collection
MOSFLM data reduction
PHASER phasing