3G29

Crystal structure of the C-terminal domain of the Rous Sarcoma Virus capsid protein: D179N mutant, neutral pH


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.9
Temperature 291.0
Details 0.20M Tris/HCl, pH7.9, 1.5M Ammonium Citrate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 99.32 α = 90
b = 99.32 β = 90
c = 34.5 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate Rigaku Varimax HF confocal 2008-10-16
Diffraction Radiation
Monochromator Protocol
Rigaku Varimax HF confocal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178 -- --

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
2.5 44 100.0 0.08 -- -- 13.7 6394 6394 0.0 0.0 --
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)
2.5 2.59 100.0 0.394 -- 2.2 13.9 604

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 2.5 44.0 0.0 0.0 6023 6023 341 99.97 0.26494 0.26494 0.26173 0.32246 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 2.5 2.565 -- 24 427 0.293 0.484 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 32.099
Anisotropic B[1][1] 0.95
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.95
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.89
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.301
r_dihedral_angle_3_deg 17.578
r_chiral_restr 0.09
r_dihedral_angle_4_deg 23.294
r_dihedral_angle_1_deg 5.252
r_dihedral_angle_2_deg 33.269
r_angle_refined_deg 1.251
r_scbond_it 1.35
r_mcbond_it 0.483
r_mcangle_it 0.909
r_bond_refined_d 0.011
r_gen_planes_refined 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1198
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 7

Software

Software
Software Name Purpose
MAR345dtb data collection
PHASER phasing
REFMAC refinement version: 5.5.0044
HKL-2000 data reduction
HKL-2000 data scaling