X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.8
Temperature 294.0
Details 100 mM sodium citrate, pH 5.8, 13.5% PEG4000, 10% isopropanol, 5% dioxane, 88 mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 281.56 α = 90
b = 125.08 β = 103.32
c = 71.08 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 ADSC QUANTUM 315 -- 2012-02-02
Diffraction Radiation
Monochromator Protocol
single crystal Si(220) side bounce SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792 APS 24-ID-E

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
2.7 40 99.5 0.079 -- -- 4.1 65155 64845 0.0 0.0 --
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)
2.7 2.8 99.0 0.556 -- -- 4.0 6400

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 2.703 37.073 0.0 0.0 64763 64763 1901 98.66 0.1943 0.1943 0.1927 0.2462 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 2.703 2.7702 -- 123 4022 0.2916 0.3671 -- 88.0
X Ray Diffraction 2.7702 2.845 -- 125 4483 0.2737 0.3604 -- 99.0
X Ray Diffraction 2.845 2.9287 -- 149 4477 0.2456 0.3301 -- 99.0
X Ray Diffraction 2.9287 3.0232 -- 139 4486 0.2249 0.2966 -- 99.0
X Ray Diffraction 3.0232 3.1312 -- 142 4524 0.2177 0.3068 -- 99.0
X Ray Diffraction 3.1312 3.2565 -- 141 4500 0.2036 0.2509 -- 100.0
X Ray Diffraction 3.2565 3.4046 -- 130 4500 0.2194 0.3072 -- 99.0
X Ray Diffraction 3.4046 3.584 -- 136 4560 0.1981 0.2363 -- 100.0
X Ray Diffraction 3.584 3.8083 -- 138 4490 0.1762 0.2068 -- 100.0
X Ray Diffraction 3.8083 4.102 -- 137 4539 0.1761 0.2313 -- 100.0
X Ray Diffraction 4.102 4.5142 -- 133 4562 0.1657 0.2085 -- 100.0
X Ray Diffraction 4.5142 5.1659 -- 136 4556 0.1563 0.231 -- 100.0
X Ray Diffraction 5.1659 6.5028 -- 134 4591 0.2098 0.2418 -- 100.0
X Ray Diffraction 6.5028 37.0768 -- 138 4572 0.1812 0.2198 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 70.5395
Anisotropic B[1][1] 6.8972
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -4.4035
Anisotropic B[2][2] -6.0097
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.8876
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.171
f_plane_restr 0.006
f_chiral_restr 0.081
f_angle_d 1.214
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12498
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 43

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
Phaser Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALEPACK data reduction