X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 277.0
Details 25% 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 = 31.02 α = 90
b = 81.29 β = 90.05
c = 60.38 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 2008-02-06
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
2 60.38 99.9 0.0635 0.0226 -- 11.3 17596 17583 0.0 0.0 20.5
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 2.1 2296.0 0.0996 0.0594 15.41 4.85 2296

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 2.1 60.38 -- 0.0 17570 17554 1781 99.91 0.2423 0.239 0.233 0.29 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 2.1 2.155 1316 121 1195 0.205 0.326 -- 100.0
X Ray Diffraction 2.155 2.214 1277 134 -- 0.195 0.247 -- 100.0
X Ray Diffraction 2.214 2.278 1204 119 -- 0.212 0.34 -- 99.917
X Ray Diffraction 2.278 2.348 1188 106 -- 0.219 0.308 -- 100.0
X Ray Diffraction 2.348 2.425 1160 107 -- 0.235 0.287 -- 99.914
X Ray Diffraction 2.425 2.51 1106 101 -- 0.242 0.285 -- 99.91
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 8.908
Anisotropic B[1][1] -0.01
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 1.837
r_scbond_it 1.198
r_mcangle_it 0.788
r_mcbond_it 0.545
r_symmetry_hbond_refined 0.147
r_symmetry_vdw_refined 0.19
r_bond_refined_d 0.009
r_angle_refined_deg 1.316
r_dihedral_angle_1_deg 6.15
r_dihedral_angle_2_deg 34.225
r_dihedral_angle_3_deg 16.847
r_dihedral_angle_4_deg 11.916
r_chiral_restr 0.083
r_gen_planes_refined 0.004
r_nbd_refined 0.202
r_nbtor_refined 0.298
r_xyhbond_nbd_refined 0.147
r_metal_ion_refined 0.044
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.292
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2060
Nucleic Acid Atoms 0
Heterogen Atoms 52
Solvent Atoms 183

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: 3.005 data extraction
REFMAC5 refinement
Phaser molecular replacement
SAINT version: V7.51A collection/data indexing