X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8
Temperature 289.0
Details 10mg/ml solution of PFV-Gag-NtD in 150mM NaCl, 5% glycerol, 10mM Tris-HCl, pH 8.0 was mixed with an equal volume of crystallisation solution containing 16% PEG 6000 (w/v), 12% ethylene glycol, 0.03M MgCl2 hexahydrate , VAPOR DIFFUSION, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 35.42 α = 90
b = 94.73 β = 93.68
c = 61.66 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
PIXEL PSI PILATUS 6M -- 2011-02-25
Diffraction Radiation
Monochromator Protocol
Double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I03 0.9791 Diamond I03

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
2.4 25 98.1 0.061 -- -- 3.2 -- n/a 1.0 1.0 --
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)
2.4 2.49 95.8 0.11 -- -- 2.8 2993

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 2.402 23.682 -- 0.0 30639 30630 1518 98.2 0.1749 0.1749 0.172 0.2298 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 2.402 2.4795 -- 152 2566 0.1778 0.2576 -- 96.0
X Ray Diffraction 2.4795 2.568 -- 105 2643 0.2012 0.2894 -- 97.0
X Ray Diffraction 2.568 2.6707 -- 107 2668 0.2058 0.3038 -- 98.0
X Ray Diffraction 2.6707 2.7921 -- 118 2675 0.2084 0.2653 -- 98.0
X Ray Diffraction 2.7921 2.939 -- 143 2667 0.1988 0.301 -- 98.0
X Ray Diffraction 2.939 3.1228 -- 158 2610 0.1935 0.274 -- 99.0
X Ray Diffraction 3.1228 3.3633 -- 146 2662 0.1763 0.2559 -- 99.0
X Ray Diffraction 3.3633 3.7006 -- 151 2638 0.1687 0.2031 -- 99.0
X Ray Diffraction 3.7006 4.2334 -- 145 2705 0.1288 0.172 -- 100.0
X Ray Diffraction 4.2334 5.3236 -- 143 2667 0.13 0.1816 -- 99.0
X Ray Diffraction 5.3236 23.6834 -- 150 2611 0.193 0.2132 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.0467
Anisotropic B[1][1] -2.0111
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.3564
Anisotropic B[2][2] 5.1634
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.1523
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.46
f_bond_d 0.008
f_chiral_restr 0.065
f_plane_restr 0.004
f_angle_d 1.044
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2804
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 171

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: 1.7_650
PDB_EXTRACT data extraction version: 3.11
GDA data collection
SOLVE phasing