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_metal_ion_refined 0.246
r_dihedral_angle_1_deg 4.949
r_bond_refined_d 0.008
r_nbd_refined 0.175
r_symmetry_vdw_refined 0.159
r_scangle_it 2.162
r_mcangle_it 0.896
r_nbtor_refined 0.289
r_symmetry_hbond_refined 0.096
r_xyhbond_nbd_refined 0.156
r_gen_planes_refined 0.003
r_chiral_restr 0.074
r_angle_refined_deg 0.996
r_dihedral_angle_3_deg 14.999
r_scbond_it 1.316
r_dihedral_angle_2_deg 39.299
r_mcbond_it 0.541
r_dihedral_angle_4_deg 19.504
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

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling version: 3.3.15
MOLREP phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10
Blu-Ice data collection