X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.5
Temperature 291.0
Details 1.2 M sodium citrate, 0.1 M HEPES, 10-fold excess SAM, pH 7.5, VAPOR DIFFUSION, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 101.44 α = 90
b = 101.44 β = 90
c = 140.8 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-300 -- 2012-01-25
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-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 87.85 100.0 -- 0.112 -- 21.6 29619 29619 -- -- --
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)
2.0 2.11 100.0 0.942 0.942 0.8 22.0 4231

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 2.0 43.96 -- 0.0 -- 29561 1516 99.97 -- 0.1769 0.1757 0.1985 THIN SHELLS (SFTOOLS)
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 2.0 2.052 -- 2 2116 0.222 0.321 -- 99.95
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 37.7619
Anisotropic B[1][1] -0.14
Anisotropic B[1][2] -0.14
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.14
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.44
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 2.38
r_mcbond_other 1.645
r_bond_refined_d 0.015
r_bond_other_d 0.002
r_angle_refined_deg 1.481
r_angle_other_deg 0.72
r_dihedral_angle_1_deg 6.144
r_dihedral_angle_2_deg 30.14
r_dihedral_angle_3_deg 11.84
r_dihedral_angle_4_deg 18.086
r_chiral_restr 0.086
r_gen_planes_refined 0.005
r_gen_planes_other 0.001
r_mcbond_it 1.645
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2440
Nucleic Acid Atoms 0
Heterogen Atoms 76
Solvent Atoms 130

Software

Computing
Computing Package Purpose
xds Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
phaser Structure Solution
REFMAC 5.7.0032 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.7.0032 refinement
Phaser molecular replacement
SCALA version: 3.3.20 data reduction