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, 10 mM calcium chloride, 4% PEG 400, soaked in 20 mM EDTA, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 181.07 α = 90
b = 181.07 β = 90
c = 181.07 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 -- 2011-04-17
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
2.3 104.54 100.0 -- 0.097 -- 42.0 11848 11848 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)
2.3 2.42 100.0 0.397 0.397 1.9 42.9 1680

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 2.3 90.54 -- 0.0 11848 11847 819 99.97 -- 0.2231 0.2194 0.2715 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 2.3 2.36 -- 61 797 0.253 0.303 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.9923
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.162
r_scbond_it 1.316
r_mcangle_it 0.896
r_mcbond_it 0.541
r_symmetry_hbond_refined 0.096
r_symmetry_vdw_refined 0.159
r_bond_refined_d 0.008
r_angle_refined_deg 0.996
r_dihedral_angle_1_deg 4.949
r_dihedral_angle_2_deg 39.299
r_dihedral_angle_3_deg 14.999
r_dihedral_angle_4_deg 19.504
r_chiral_restr 0.074
r_gen_planes_refined 0.003
r_nbd_refined 0.175
r_nbtor_refined 0.289
r_xyhbond_nbd_refined 0.156
r_metal_ion_refined 0.246
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1413
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 93

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