X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4
Temperature 293.0
Details 100mM Na malonate-HCl, 3.0-3.3M Na formate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 107.82 α = 90
b = 88.92 β = 94.31
c = 60.68 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 MARMOSAIC 225 mm CCD -- 2012-02-01
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
2.37 50 99.4 0.051 0.051 -- 3.8 -- 23087 0.0 -3.0 40.586
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)
2.374 2.42 89.8 0.116 0.116 11.464 3.6 1048

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 2.374 46.476 -- 1.36 23191 23058 1182 99.42 -- 0.2383 0.2358 0.2846 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 2.374 2.4818 2810 128 2682 0.2869 0.4116 -- 97.0
X Ray Diffraction 2.4818 2.6127 2857 149 2708 0.2542 0.2962 -- 100.0
X Ray Diffraction 2.6127 2.7763 2895 137 2756 0.2337 0.2953 -- 100.0
X Ray Diffraction 2.7763 2.9907 2885 150 2735 0.2475 0.3009 -- 100.0
X Ray Diffraction 2.9907 3.2915 2870 159 2711 0.2504 0.2767 -- 100.0
X Ray Diffraction 3.2915 3.7677 2896 163 2733 0.2305 0.2976 -- 100.0
X Ray Diffraction 3.7677 4.7461 2906 151 2755 0.2081 0.2877 -- 100.0
X Ray Diffraction 4.7461 46.4847 2941 145 2796 0.2397 0.2361 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 6.7307
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.3997
Anisotropic B[2][2] -4.2974
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.4333
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.008
f_chiral_restr 0.073
f_dihedral_angle_d 15.578
f_angle_d 1.296
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2759
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 101

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