2V4X

Crystal Structure of Jaagsiekte Sheep Retrovirus Capsid N-terminal domain


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 29.59 α = 90
b = 57.83 β = 109.17
c = 40.93 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 CCD -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX14.1 -- SRS PX14.1

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
1.5 20 98.8 0.08 -- -- 5.0 -- 20920 -- -- --
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)
1.5 1.55 90.2 0.4 -- 2.9 4.2 --

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
SAD 1.5 14.79 -- -- -- 19678 1067 99.2 -- 0.152 0.15 0.185 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 1.5 1.54 -- 72 1340 0.214 0.242 -- 92.05
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 7.96
Anisotropic B[1][1] 1.49
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.98
Anisotropic B[2][2] -0.64
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.2
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 0.993
r_scbond_it 2.015
r_symmetry_vdw_other 0.234
r_xyhbond_nbd_refined 0.132
r_angle_refined_deg 1.177
r_chiral_restr 0.069
r_symmetry_vdw_refined 0.18
r_nbd_refined 0.228
r_bond_refined_d 0.009
r_dihedral_angle_4_deg 17.31
r_bond_other_d 0.005
r_nbtor_other 0.085
r_gen_planes_refined 0.005
r_nbd_other 0.182
r_symmetry_hbond_refined 0.119
r_mcbond_it 0.79
r_scangle_it 2.837
r_gen_planes_other 0.001
r_angle_other_deg 0.871
r_nbtor_refined 0.193
r_dihedral_angle_1_deg 4.626
r_dihedral_angle_2_deg 39.542
r_dihedral_angle_3_deg 13.156
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1043
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 201

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing