X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 277.0
Details 17% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 8.0, vapor diffusion, hanging drop, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 31.1 α = 90
b = 60.65 β = 94.44
c = 36.95 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD BRUKER APEX II multi-layer optics 2007-09-05
Diffraction Radiation
Monochromator Protocol
GE111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SEALED TUBE OTHER 1.5418 -- --

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
1.8 31.5 99.37 -- 0.152 -- 13.18 -- 14206 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)
1.8 1.9 100.0 -- 0.415 6.22 7.86 --

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 1.8 31.01 -- -- 12767 10735 1179 93.32 -- 0.19556 0.1895 0.2512 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 1.8 1.847 -- 83 737 0.273 0.362 -- 85.15
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 22.944
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.01
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.01
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.785
r_scbond_it 2.535
r_mcangle_it 1.629
r_mcbond_it 1.11
r_nbd_refined 0.23
r_gen_planes_refined 0.006
r_chiral_restr 0.121
r_dihedral_angle_4_deg 9.345
r_dihedral_angle_3_deg 16.675
r_dihedral_angle_2_deg 34.112
r_dihedral_angle_1_deg 5.907
r_angle_refined_deg 1.772
r_bond_refined_d 0.017
r_nbtor_refined 0.31
r_xyhbond_nbd_refined 0.139
r_symmetry_vdw_refined 0.121
r_symmetry_hbond_refined 0.135
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1033
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 106

Software

Computing
Computing Package Purpose
APEX Data Collection
SAINT Data Reduction (intensity integration)
SAINT Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.000 data extraction
REFMAC5 version: 5.2.0019 refinement
Phaser molecular replacement
SAINT version: V7.34A data processing
SAINT collection/data indexing