X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 290.0
Details 25% PEG 6000, 0.2M ammonium formate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45 α = 90
b = 57.47 β = 90
c = 66.15 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
AREA DETECTOR RIGAKU RAXIS IV++ -- 2011-11-21
Diffraction Radiation
Monochromator Protocol
osmic mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH2R 1.54 -- --

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
1.77 50 99.1 0.047 -- -- 3.2 17399 17235 -3.0 -3.0 --
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)
1.77 1.83 95.5 0.512 -- -- 2.9 1624

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 1.85 31.232 -- 0.0 15128 14821 1484 97.47 0.2045 0.2045 0.2006 0.2396 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 1.85 1.9097 -- 129 1151 0.2199 0.3095 -- 93.0
X Ray Diffraction 1.9097 1.978 -- 130 1152 0.1977 0.2699 -- 94.0
X Ray Diffraction 1.978 2.0572 -- 131 1179 0.1886 0.2693 -- 96.0
X Ray Diffraction 2.0572 2.1508 -- 132 1197 0.2 0.2634 -- 98.0
X Ray Diffraction 2.1508 2.2641 -- 131 1183 0.2029 0.2646 -- 98.0
X Ray Diffraction 2.2641 2.4059 -- 137 1217 0.2019 0.2395 -- 99.0
X Ray Diffraction 2.4059 2.5916 -- 136 1233 0.1986 0.2165 -- 99.0
X Ray Diffraction 2.5916 2.8523 -- 135 1220 0.2012 0.2826 -- 99.0
X Ray Diffraction 2.8523 3.2646 -- 138 1235 0.2108 0.2389 -- 99.0
X Ray Diffraction 3.2646 4.1116 -- 139 1259 0.1856 0.2135 -- 98.0
X Ray Diffraction 4.1116 31.2359 -- 146 1311 0.2082 0.2321 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.0771
Anisotropic B[1][1] 8.4058
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.5709
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.8349
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 18.296
f_plane_restr 0.004
f_chiral_restr 0.081
f_angle_d 1.125
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1174
Nucleic Acid Atoms 204
Heterogen Atoms 0
Solvent Atoms 123

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX (phenix.refine: 1.7_650) Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction