X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 293.0
Details 16% polyethylene glycol 8000, 0.1 M sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 82.7 α = 90
b = 104.76 β = 103.87
c = 101.56 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2011-05-20
Diffraction Radiation
Monochromator Protocol
Double-crystal, Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.2 1.0000 ALS 5.0.2

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 50 100.0 0.067 -- -- 3.8 113395 113395 -- -3.0 --
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)
2.0 2.07 100.0 0.546 -- -- 3.8 --

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 49.33 -- -- 113412 107626 5714 99.94 -- 0.19657 0.19482 0.22948 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 2.0 2.052 -- 463 7892 0.246 0.295 -- 99.98
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 47.52
Anisotropic B[1][1] -0.77
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.17
Anisotropic B[2][2] 0.96
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.11
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.954
r_scbond_it 1.266
r_mcangle_it 1.609
r_mcbond_it 0.966
r_nbd_refined 0.178
r_gen_planes_refined 0.003
r_chiral_restr 0.071
r_dihedral_angle_4_deg 14.981
r_dihedral_angle_3_deg 12.541
r_dihedral_angle_2_deg 33.92
r_dihedral_angle_1_deg 6.019
r_angle_refined_deg 1.125
r_bond_refined_d 0.008
r_nbtor_refined 0.306
r_xyhbond_nbd_refined 0.111
r_symmetry_vdw_refined 0.199
r_symmetry_hbond_refined 0.156
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8826
Nucleic Acid Atoms 0
Heterogen Atoms 156
Solvent Atoms 952

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
SCALEPACK data reduction