X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.8
Temperature 293.0
Details 0.2M Sodium citrate, 1M Ammonium sulphate, 0.1M Copper chloride, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 81.56 α = 90
b = 81.56 β = 90
c = 68.82 γ = 120
Symmetry
Space Group P 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate Mirrors 2009-01-07
Diffraction Radiation
Monochromator Protocol
Mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE BRUKER AXS MICROSTAR 1.54 -- --

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
2.2 30 99.8 0.0649 0.0567 -- 5.41 -- 24706 -- -- 28.26
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)
2.2 2.3 99.1 0.2311 0.2022 1.1 5.01 65208

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 2.2 26.7 -- -- -- 24706 1286 99.9 -- 0.26945 0.26797 0.29882 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 2.2 2.257 -- 82 1818 0.436 0.527 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.186
Anisotropic B[1][1] -0.21
Anisotropic B[1][2] -0.11
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.21
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.32
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.019
r_mcangle_it 1.744
r_nbd_refined 0.272
r_symmetry_vdw_refined 0.348
r_mcbond_it 1.12
r_dihedral_angle_3_deg 21.093
r_dihedral_angle_1_deg 8.33
r_dihedral_angle_4_deg 18.834
r_gen_planes_refined 0.007
r_angle_refined_deg 1.826
r_symmetry_metal_ion_refined 0.009
r_metal_ion_refined 0.015
r_nbtor_refined 0.309
r_dihedral_angle_2_deg 39.15
r_symmetry_hbond_refined 0.311
r_scbond_it 2.779
r_scangle_it 3.805
r_chiral_restr 0.123
r_xyhbond_nbd_refined 0.241
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4821
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 310

Software

Software
Software Name Purpose
MAR345dtb data collection
AMoRE phasing
REFMAC refinement version: 5.2.0019
AUTOMAR data reduction
SCALEPACK data scaling