X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 298.0
Details 50 mM Tris, 5 mM calcium chloride, 200 microM cupric chloride , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 179.27 α = 90
b = 179.27 β = 90
c = 179.27 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
AREA DETECTOR MARMOSAIC 325 mm CCD -- 2012-01-23
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
1.85 103.5 100.0 -- 0.06 -- 15.2 21660 21660 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)
1.85 1.95 100.0 0.215 0.215 3.2 15.2 3115

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 1.85 51.78 -- 0.0 21641 21639 1573 99.98 0.1709 0.1709 0.1688 0.1968 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 1.851 1.899 -- 103 1470 0.198 0.234 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.5534
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.762
r_scbond_it 1.076
r_mcangle_it 0.587
r_mcbond_it 0.356
r_symmetry_metal_ion_refined 0.045
r_symmetry_hbond_refined 0.09
r_symmetry_vdw_refined 0.185
r_bond_refined_d 0.006
r_angle_refined_deg 0.842
r_dihedral_angle_1_deg 4.429
r_dihedral_angle_2_deg 36.803
r_dihedral_angle_3_deg 11.114
r_dihedral_angle_4_deg 17.995
r_chiral_restr 0.069
r_gen_planes_refined 0.003
r_nbd_refined 0.175
r_nbtor_refined 0.29
r_xyhbond_nbd_refined 0.081
r_metal_ion_refined 0.082
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1416
Nucleic Acid Atoms 0
Heterogen Atoms 7
Solvent Atoms 215

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