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, 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
CCD 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_dihedral_angle_4_deg 17.995
r_dihedral_angle_3_deg 11.114
r_chiral_restr 0.069
r_scbond_it 1.076
r_symmetry_hbond_refined 0.09
r_mcbond_it 0.356
r_scangle_it 1.762
r_mcangle_it 0.587
r_dihedral_angle_2_deg 36.803
r_bond_refined_d 0.006
r_nbtor_refined 0.29
r_dihedral_angle_1_deg 4.429
r_gen_planes_refined 0.003
r_symmetry_vdw_refined 0.185
r_symmetry_metal_ion_refined 0.045
r_angle_refined_deg 0.842
r_nbd_refined 0.175
r_metal_ion_refined 0.082
r_xyhbond_nbd_refined 0.081
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

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