X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Details 0.1 M TRIS-HCL, PH 7.5, 0.1 M SODIUM CITRATE, 18 %(W/V) PEG 400. PROTEIN WAS MIXED WITH 7.8 MAG AT RATIO 1:1 (W:W) TO FORM CUBIC PHASE.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.25 α = 90
b = 74.42 β = 101.56
c = 115.53 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2008-04-22
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL CRYO-COOLED SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B -- APS 23-ID-B

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
1.9 113.18 100.0 0.14 -- -- 6.4 -- 37703 -- -3.0 15.42
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 1.97 84.9 0.35 -- 2.9 2.5 --

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 1.897 19.77 -- 0.0 -- 35580 1788 94.51 -- 0.1656 0.1633 0.2086 --
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 1.8973 1.9486 -- 98 1972 0.2185 0.3114 -- 71.0
X Ray Diffraction 1.9486 2.0059 -- 129 2306 0.1739 0.2219 -- 86.0
X Ray Diffraction 2.0059 2.0705 -- 124 2526 0.1611 0.2108 -- 91.0
X Ray Diffraction 2.0705 2.1444 -- 122 2591 0.1574 0.228 -- 94.0
X Ray Diffraction 2.1444 2.2302 -- 130 2615 0.1533 0.1961 -- 95.0
X Ray Diffraction 2.2302 2.3315 -- 137 2647 0.1582 0.2298 -- 97.0
X Ray Diffraction 2.3315 2.4543 -- 161 2674 0.1566 0.2297 -- 97.0
X Ray Diffraction 2.4543 2.6077 -- 138 2719 0.1547 0.1984 -- 98.0
X Ray Diffraction 2.6077 2.8085 -- 143 2688 0.1633 0.2182 -- 99.0
X Ray Diffraction 2.8085 3.0902 -- 141 2734 0.1646 0.1917 -- 99.0
X Ray Diffraction 3.0902 3.5352 -- 160 2736 0.1601 0.2039 -- 100.0
X Ray Diffraction 3.5352 4.4456 -- 155 2770 0.1543 0.1976 -- 100.0
X Ray Diffraction 4.4456 19.7712 -- 150 2814 0.1763 0.1942 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.505
Anisotropic B[1][1] 1.0359
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.7468
Anisotropic B[2][2] 2.2185
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.2544
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.099
f_dihedral_angle_d 19.379
f_angle_d 1.344
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3415
Nucleic Acid Atoms 0
Heterogen Atoms 342
Solvent Atoms 242

Software

Computing
Computing Package Purpose
HKL2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (PHENIX.REFINE) Structure Refinement
Software
Software Name Purpose
PHENIX version: (PHENIX.REFINE) refinement
PHASER model building