X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 277.0
Details Jeffamine M-600, CsCl, pH 6.5, temperature 277K, VAPOR DIFFUSION, HANGING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 125.6 α = 90
b = 221.9 β = 90
c = 106.8 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC CCD300 -- 2010-01-27
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97934 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
3.8 19.92 80.4 -- -- -- 4.0 24030 24030 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)
3.8 3.9 34.1 -- -- 3.3 4.1 760

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 3.8 19.92 -- 0.0 24030 24030 1189 80.39 0.3009 0.3009 0.2987 0.3434 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 3.8 3.895 760 28 682 0.414 0.456 -- 33.65
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 159.652
Anisotropic B[1][1] 9.3
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -15.6
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 6.31
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.507
r_scbond_it 0.796
r_mcangle_it 1.348
r_mcbond_other 0.074
r_bond_refined_d 0.013
r_bond_other_d 0.005
r_angle_refined_deg 1.336
r_angle_other_deg 0.919
r_dihedral_angle_1_deg 6.83
r_dihedral_angle_2_deg 38.571
r_dihedral_angle_3_deg 19.101
r_dihedral_angle_4_deg 17.241
r_chiral_restr 0.071
r_gen_planes_refined 0.006
r_gen_planes_other 0.002
r_mcbond_it 0.745
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12978
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 0

Software

Computing
Computing Package Purpose
MxDC Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.5.0102 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
Phaser molecular replacement