X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

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_bond_other_d 0.002
r_mcangle_it 2.38
r_gen_planes_other 0.001
r_angle_other_deg 0.72
r_mcbond_it 1.645
r_chiral_restr 0.086
r_dihedral_angle_2_deg 30.14
r_dihedral_angle_4_deg 18.086
r_gen_planes_refined 0.005
r_dihedral_angle_3_deg 11.84
r_bond_refined_d 0.015
r_mcbond_other 1.645
r_dihedral_angle_1_deg 6.144
r_angle_refined_deg 1.481
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

Software
Software Name Purpose
SCALA data scaling version: 3.3.20
PHASER phasing
REFMAC refinement version: 5.7.0032
PDB_EXTRACT data extraction version: 3.11
XDS data reduction