X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.5
Temperature 298.0
Details 15% PEG 4000, 300mM MgCl2, 100mM Tris, pH 7.5, vapor diffusion, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 75.36 α = 90
b = 78.16 β = 90
c = 93.77 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2013-02-25
Diffraction Radiation
Monochromator Protocol
Si SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08B1-1 0.97949 CLSI 08B1-1

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
1.3 50 99.4 0.041 -- -- 5.5 -- 135702 1.0 1.0 --
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)
1.3 1.35 100.0 0.568 -- -- 5.4 13514

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 1.3 40.04 -- 0.0 -- 123935 6249 90.53 -- 0.1207 0.1194 0.1453 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 1.3 1.332 -- 168 2773 0.126 0.175 -- 29.59
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.2539
Anisotropic B[1][1] -0.24
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.15
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.39
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 14.405
r_sphericity_free 31.477
r_bond_refined_d 0.011
r_bond_other_d 0.001
r_angle_refined_deg 1.442
r_angle_other_deg 0.764
r_dihedral_angle_1_deg 5.788
r_dihedral_angle_2_deg 39.141
r_dihedral_angle_3_deg 12.653
r_dihedral_angle_4_deg 15.633
r_chiral_restr 0.083
r_gen_planes_refined 0.007
r_gen_planes_other 0.001
r_rigid_bond_restr 2.84
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3595
Nucleic Acid Atoms 0
Heterogen Atoms 25
Solvent Atoms 691

Software

Computing
Computing Package Purpose
CLS Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
REFMAC 5.6.0117 Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
SCALEPACK data reduction
DENZO data collection