X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

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_dihedral_angle_2_deg 34.225
r_dihedral_angle_1_deg 6.15
r_nbd_refined 0.202
r_chiral_restr 0.083
r_metal_ion_refined 0.044
r_mcbond_it 0.545
r_dihedral_angle_3_deg 16.847
r_dihedral_angle_4_deg 11.916
r_mcangle_it 0.788
r_nbtor_refined 0.298
r_symmetry_hbond_refined 0.147
r_bond_refined_d 0.009
r_xyhbond_nbd_refined 0.147
r_gen_planes_refined 0.004
r_scangle_it 1.837
r_symmetry_vdw_refined 0.19
r_scbond_it 1.198
r_angle_refined_deg 1.316
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

Software
Software Name Purpose
SAINT data scaling version: V7.51A
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.005
APEX data collection
SAINT data reduction