X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Microbatch Under Oil
pH 6
Temperature 298.0
Details PEG 3350, sodium malonate, pH 6.0, microbatch under oil, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 79.11 α = 90
b = 101.47 β = 90
c = 130.54 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 200
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 mirrors 2012-02-18
Diffraction Radiation
Monochromator Protocol
Yale mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 1.127 SSRL BL7-1

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 65.3 98.4 0.082 -- -- 7.1 16524 16260 -- 2.0 --
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)
2.6 2.67 97.5 0.516 -- 2.3 4.5 --

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
PHASER 2.602 65.27 -- -- -- 15432 819 98.39 -- 0.22355 0.21999 0.29814 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 2.602 2.669 -- 44 1044 0.291 0.435 -- 97.49
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 93.672
Anisotropic B[1][1] 0.09
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.04
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.008
r_chiral_restr 0.101
r_dihedral_angle_4_deg 18.884
r_dihedral_angle_3_deg 19.75
r_dihedral_angle_2_deg 38.998
r_dihedral_angle_1_deg 6.541
r_angle_refined_deg 1.998
r_bond_refined_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3749
Nucleic Acid Atoms 0
Heterogen Atoms 43
Solvent Atoms 6

Software

Computing
Computing Package Purpose
Blu-Ice Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.6.0117 refinement
PHASER model building
Blu-Ice data collection