X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.2
Temperature 293.0
Details 0.49M NaH2PO4, 0.91M K2HPO4, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.86 α = 90
b = 127.42 β = 113.84
c = 97.22 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 MARMOSAIC 225 mm CCD mirrors 2009-07-14
Diffraction Radiation
Monochromator Protocol
Si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.0000 SPRING-8 BL26B2

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
2.6 50 98.5 0.063 0.063 -- 3.6 -- 61981 0.0 -3.0 66.659
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)
2.6 2.69 89.5 0.669 0.669 1.625 3.6 5598

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 2.6 30.7 -- 1.34 61972 61951 3144 98.69 -- 0.2267 0.2247 0.2641 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 2.6 2.633 2323 119 2204 0.3643 0.4382 -- 81.0
X Ray Diffraction 2.633 2.6761 2775 143 2632 0.3358 0.3459 -- 98.0
X Ray Diffraction 2.6761 2.7222 2807 131 2676 0.3276 0.4065 -- 99.0
X Ray Diffraction 2.7222 2.7717 2847 166 2681 0.3132 0.3714 -- 99.0
X Ray Diffraction 2.7717 2.825 2808 132 2676 0.3004 0.337 -- 99.0
X Ray Diffraction 2.825 2.8826 2807 139 2668 0.2778 0.3159 -- 100.0
X Ray Diffraction 2.8826 2.9452 2840 147 2693 0.2866 0.3546 -- 99.0
X Ray Diffraction 2.9452 3.0137 2833 127 2706 0.2773 0.2965 -- 99.0
X Ray Diffraction 3.0137 3.089 2806 152 2654 0.2707 0.2871 -- 99.0
X Ray Diffraction 3.089 3.1724 2842 144 2698 0.2645 0.3175 -- 99.0
X Ray Diffraction 3.1724 3.2657 2849 153 2696 0.2654 0.3433 -- 99.0
X Ray Diffraction 3.2657 3.3709 2824 140 2684 0.2377 0.2789 -- 100.0
X Ray Diffraction 3.3709 3.4913 2845 151 2694 0.2322 0.2816 -- 100.0
X Ray Diffraction 3.4913 3.6308 2859 135 2724 0.2178 0.2408 -- 100.0
X Ray Diffraction 3.6308 3.7958 2814 141 2673 0.216 0.242 -- 100.0
X Ray Diffraction 3.7958 3.9955 2847 141 2706 0.1977 0.2277 -- 100.0
X Ray Diffraction 3.9955 4.2453 2862 131 2731 0.1831 0.2339 -- 100.0
X Ray Diffraction 4.2453 4.5721 2861 161 2700 0.1772 0.2297 -- 100.0
X Ray Diffraction 4.5721 5.0304 2846 131 2715 0.1914 0.2166 -- 100.0
X Ray Diffraction 5.0304 5.7541 2873 159 2724 0.2311 0.298 -- 100.0
X Ray Diffraction 5.7541 7.2339 2865 142 2723 0.2459 0.281 -- 100.0
X Ray Diffraction 7.2339 30.7026 2908 159 2749 0.1768 0.1939 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 14.6874
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 9.8465
Anisotropic B[2][2] -16.2021
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.5148
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.072
f_dihedral_angle_d 15.47
f_angle_d 1.181
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7499
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 43

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX Structure Refinement
Software
Software Name Purpose
PHENIX refinement
PHENIX model building
HKL-2000 data collection