X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 289.0
Details 0.2 M sodium chloride, 0.1 M HEPES pH 7.5, 25 % w/v Polyethylene glycol 3,350, 10 mM manganese chloride, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 39.1 α = 90
b = 78.61 β = 90
c = 133.71 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r mirrors 2011-10-09
Diffraction Radiation
Monochromator Protocol
duoble crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97924 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
1.5 50 100.0 -- 0.085 -- 7.8 67113 67113 0.0 0.0 17.64
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 1.53 100.0 -- 0.664 2.8 6.9 3259

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 1.498 38.771 -- 0.0 67022 67022 3398 99.64 0.122 0.122 0.12 0.158 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 1.4978 1.5192 2554 113 2441 0.1442 0.2414 -- 92.0
X Ray Diffraction 1.5192 1.5419 2733 151 2582 0.133 0.193 -- 100.0
X Ray Diffraction 1.5419 1.566 2794 140 2654 0.1231 0.2124 -- 100.0
X Ray Diffraction 1.566 1.5917 2710 123 2597 0.1158 0.1847 -- 100.0
X Ray Diffraction 1.5917 1.6191 2785 167 2618 0.1141 0.1929 -- 100.0
X Ray Diffraction 1.6191 1.6486 2756 137 2619 0.1099 0.1975 -- 100.0
X Ray Diffraction 1.6486 1.6803 2777 147 2630 0.1038 0.1792 -- 100.0
X Ray Diffraction 1.6803 1.7146 2759 130 2629 0.0987 0.1629 -- 100.0
X Ray Diffraction 1.7146 1.7519 2765 143 2622 0.1013 0.1599 -- 100.0
X Ray Diffraction 1.7519 1.7926 2793 154 2639 0.1053 0.1692 -- 100.0
X Ray Diffraction 1.7926 1.8375 2770 133 2637 0.0982 0.1737 -- 100.0
X Ray Diffraction 1.8375 1.8871 2780 168 2612 0.0953 0.1463 -- 100.0
X Ray Diffraction 1.8871 1.9427 2788 163 2625 0.0952 0.1521 -- 100.0
X Ray Diffraction 1.9427 2.0054 2773 137 2636 0.0958 0.1381 -- 100.0
X Ray Diffraction 2.0054 2.077 2805 143 2662 0.0961 0.147 -- 100.0
X Ray Diffraction 2.077 2.1602 2797 143 2654 0.1002 0.1504 -- 100.0
X Ray Diffraction 2.1602 2.2585 2795 137 2658 0.1054 0.1558 -- 100.0
X Ray Diffraction 2.2585 2.3776 2801 151 2650 0.1102 0.1583 -- 100.0
X Ray Diffraction 2.3776 2.5265 2816 142 2674 0.1191 0.1588 -- 100.0
X Ray Diffraction 2.5265 2.7215 2830 147 2683 0.1251 0.142 -- 100.0
X Ray Diffraction 2.7215 2.9953 2848 133 2715 0.137 0.157 -- 100.0
X Ray Diffraction 2.9953 3.4285 2849 126 2723 0.1339 0.1626 -- 100.0
X Ray Diffraction 3.4285 4.3186 2913 118 2795 0.1233 0.1613 -- 100.0
X Ray Diffraction 4.3186 38.7845 3021 152 2869 0.1431 0.1465 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.079
f_dihedral_angle_d 14.527
f_angle_d 1.132
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3586
Nucleic Acid Atoms 0
Heterogen Atoms 74
Solvent Atoms 469

Software

Computing
Computing Package Purpose
SBCCOLLECT, HKL3000 Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
HKL3000, Molrep Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8_1069) refinement
Molrep model building
HKL3000 model building
HKL3000 data collection
SBCCOLLECT data collection