X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Precipitation
pH 8
Temperature 277.0
Details 150 mM NaCl, 40 mM Tris-HCl, 5 % w/v glycerol, 2.5 mM CaCl2, pH 8.0, precipitation, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 128.72 α = 90
b = 128.72 β = 90
c = 137.51 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2008-11-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 0.9330 ESRF ID14-2

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
2.8 46.98 99.5 0.135 -- -- 11.17 31845 31686 0.0 -3.0 32.789
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)
2.8 3.0 93.7 0.372 -- 7.7 -- 5569

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 2.8 46.984 7.7 0.0 31845 30225 1606 99.96 0.239 0.239 0.237 0.269 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 2.8 2.873 2223 116 2223 0.32 0.346 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.078
Anisotropic B[1][1] -0.04
Anisotropic B[1][2] -0.02
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.04
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.06
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 1.303
r_angle_refined_deg 1.579
r_dihedral_angle_1_deg 5.647
r_bond_refined_d 0.015
r_chiral_restr 0.162
r_dihedral_angle_3_deg 19.524
r_nbtor_refined 0.312
r_symmetry_hbond_refined 0.249
r_dihedral_angle_4_deg 19.086
r_symmetry_vdw_refined 0.333
r_nbd_refined 0.225
r_mcangle_it 0.78
r_dihedral_angle_2_deg 34.601
r_mcbond_it 0.487
r_gen_planes_refined 0.005
r_scangle_it 2.273
r_xyhbond_nbd_refined 0.146
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8689
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 4

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.006
MxCuBE data collection
XDS data reduction