X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Batch Method
pH 6.5
Temperature 293.0
Details 20 ul Protein Solution (60mg/ml protein in 0.01 M ammonium phosphate pH 7.0) mixed with 100 ul mother liquor (0.5 ml 2M monobasic ammonium phosphate + 1.5 ml 2 M dibasic ammonium phosphate + 8 ml 4 M ammonium sulfate) for final concentrations of 2.4-2.6 M Ammonium phosphate/sulfate, Batch Method, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 62.55 α = 90
b = 81.83 β = 99.76
c = 53.45 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
IMAGE PLATE RIGAKU RAXIS -- 2009-04-20
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.5418 -- --

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
1.6 52.67 89.5 0.038 -- -- 2.83 -- 62570 -- 5.0 --
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)
1.6 1.66 72.3 0.231 -- 4.2 2.64 5038

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
FOURIER SYNTHESIS 1.6 28.817 -- 1.0 -- 61818 1993 88.01 -- 0.1741 0.1733 0.1982 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 1.6 1.6378 -- 101 3045 0.1629 0.2204 -- 63.0
X Ray Diffraction 1.6378 1.682 -- 137 4090 0.1643 0.2404 -- 85.0
X Ray Diffraction 1.682 1.7315 -- 140 4155 0.1586 0.1929 -- 86.0
X Ray Diffraction 1.7315 1.7874 -- 137 4145 0.1537 0.229 -- 85.0
X Ray Diffraction 1.7874 1.8513 -- 139 4149 0.1464 0.2009 -- 86.0
X Ray Diffraction 1.8513 1.9254 -- 138 4190 0.1465 0.1698 -- 87.0
X Ray Diffraction 1.9254 2.013 -- 143 4279 0.1444 0.2034 -- 88.0
X Ray Diffraction 2.013 2.1191 -- 146 4352 0.137 0.1741 -- 90.0
X Ray Diffraction 2.1191 2.2518 -- 150 4488 0.1285 0.1664 -- 93.0
X Ray Diffraction 2.2518 2.4256 -- 152 4601 0.1237 0.1611 -- 95.0
X Ray Diffraction 2.4256 2.6695 -- 156 4650 0.1338 0.1597 -- 96.0
X Ray Diffraction 2.6695 3.0554 -- 156 4690 0.1411 0.1602 -- 96.0
X Ray Diffraction 3.0554 3.8481 -- 153 4586 0.1417 0.1657 -- 94.0
X Ray Diffraction 3.8481 28.8221 -- 145 4405 0.1809 0.194 -- 89.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.6389
Anisotropic B[1][1] -0.5846
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.7569
Anisotropic B[2][2] 1.583
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.9984
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.013
f_angle_d 1.571
f_dihedral_angle_d 13.692
f_plane_restr 0.009
f_chiral_restr 0.081
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4392
Nucleic Acid Atoms 0
Heterogen Atoms 182
Solvent Atoms 694

Software

Software
Software Name Purpose
d*TREK data scaling
PHENIX refinement version: 1.6.1_357
PDB_EXTRACT data extraction version: 3.10
CrystalClear data collection
d*TREK data reduction
CNS phasing