X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 291.0
Details 0.1 M calcium acetate, 0.1 M cacodylate buffer, 40% PEG-3000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.43 α = 90
b = 100.71 β = 90.47
c = 70.35 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 QUANTUM 315 -- 2009-03-29
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID

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
2.15 48.6 99.3 0.094 -- -- 12.0 41638 41638 0.0 0.0 50.4
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)
2.15 2.19 92.8 0.772 -- 2.41 8.5 1935

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 2.152 48.56 0.0 1.89 81461 41550 4126 98.64 -- 0.2218 0.2198 0.2585 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 2.1518 2.1771 -- 135 2275 0.3123 0.3892 -- 84.0
X Ray Diffraction 2.1771 2.2036 -- 137 2552 0.2935 0.3451 -- 92.0
X Ray Diffraction 2.2036 2.2315 -- 136 2526 0.2906 0.3215 -- 94.0
X Ray Diffraction 2.2315 2.2609 -- 118 2552 0.2841 0.2931 -- 96.0
X Ray Diffraction 2.2609 2.2919 -- 165 2718 0.2695 0.3952 -- 99.0
X Ray Diffraction 2.2919 2.3246 -- 154 2628 0.2721 0.292 -- 99.0
X Ray Diffraction 2.3246 2.3593 -- 123 2720 0.259 0.2777 -- 100.0
X Ray Diffraction 2.3593 2.3962 -- 169 2718 0.254 0.3297 -- 100.0
X Ray Diffraction 2.3962 2.4354 -- 163 2632 0.2546 0.3244 -- 100.0
X Ray Diffraction 2.4354 2.4774 -- 142 2678 0.2357 0.3103 -- 100.0
X Ray Diffraction 2.4774 2.5225 -- 103 2786 0.2281 0.2598 -- 100.0
X Ray Diffraction 2.5225 2.571 -- 161 2626 0.2436 0.2708 -- 100.0
X Ray Diffraction 2.571 2.6235 -- 144 2747 0.24 0.313 -- 100.0
X Ray Diffraction 2.6235 2.6805 -- 136 2655 0.2334 0.311 -- 100.0
X Ray Diffraction 2.6805 2.7429 -- 150 2746 0.2462 0.2755 -- 100.0
X Ray Diffraction 2.7429 2.8114 -- 114 2721 0.2467 0.2935 -- 100.0
X Ray Diffraction 2.8114 2.8875 -- 131 2695 0.2468 0.3007 -- 100.0
X Ray Diffraction 2.8875 2.9724 -- 152 2693 0.245 0.294 -- 100.0
X Ray Diffraction 2.9724 3.0683 -- 111 2754 0.2619 0.3541 -- 100.0
X Ray Diffraction 3.0683 3.178 -- 170 2619 0.2524 0.3106 -- 100.0
X Ray Diffraction 3.178 3.3052 -- 132 2729 0.2483 0.3091 -- 100.0
X Ray Diffraction 3.3052 3.4556 -- 157 2695 0.2306 0.286 -- 100.0
X Ray Diffraction 3.4556 3.6377 -- 127 2703 0.2178 0.2175 -- 100.0
X Ray Diffraction 3.6377 3.8655 -- 166 2706 0.2012 0.2361 -- 100.0
X Ray Diffraction 3.8655 4.1638 -- 132 2671 0.1892 0.2431 -- 100.0
X Ray Diffraction 4.1638 4.5826 -- 142 2734 0.1748 0.1879 -- 100.0
X Ray Diffraction 4.5826 5.245 -- 161 2677 0.1903 0.213 -- 100.0
X Ray Diffraction 5.245 6.6055 -- 142 2700 0.2308 0.2953 -- 100.0
X Ray Diffraction 6.6055 48.5721 -- 153 2679 0.1816 0.2008 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 61.1333
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 18.973
f_plane_restr 0.002
f_chiral_restr 0.047
f_angle_d 0.702
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5373
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 91

Software

Computing
Computing Package Purpose
SBC-collect Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
SHELXD, MLPHARE, DM, SOLVE/RESOLVE, HKL-3000 Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction