X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 298.0
Details 50 mM Tris, 5 mM calcium chloride, 8% PEG 1900 MME, 700 micro M cupric chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 179.59 α = 90
b = 179.59 β = 90
c = 179.59 γ = 90
Symmetry
Space Group F 4 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD -- 2011-04-16
Diffraction Radiation
Monochromator Protocol
Rh coated flat mirror, toroidal focusing mirror SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.98 SSRL BL9-2

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
1.9 103.69 99.8 -- 0.102 -- 27.1 20095 20095 3.0 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)
1.9 2.0 100.0 0.492 0.492 1.4 20.0 --

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 1.9 89.8 -- -- 20087 18597 1454 99.72 -- 0.21935 0.21766 0.24072 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 1.9 1.951 -- 99 1345 0.321 0.331 -- 99.86
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.864
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.941
r_scbond_it 1.191
r_mcangle_it 0.718
r_mcbond_it 0.439
r_nbd_refined 0.179
r_gen_planes_refined 0.003
r_chiral_restr 0.068
r_dihedral_angle_4_deg 18.424
r_dihedral_angle_3_deg 12.027
r_dihedral_angle_2_deg 36.392
r_dihedral_angle_1_deg 4.454
r_angle_refined_deg 0.886
r_bond_refined_d 0.007
r_nbtor_refined 0.291
r_xyhbond_nbd_refined 0.275
r_metal_ion_refined 0.073
r_symmetry_vdw_refined 0.171
r_symmetry_hbond_refined 0.12
r_symmetry_metal_ion_refined 0.078
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1412
Nucleic Acid Atoms 0
Heterogen Atoms 17
Solvent Atoms 164

Software

Computing
Computing Package Purpose
BluIce Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
MOLREP molecular replacement
SCALA version: 3.3.15 data reduction
Mosflm data collection