X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 277.0
Details 35% PEG 600, 0.1 MIB pH 7.5, 7mM [Co(NH3)6]Cl3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.4 α = 90
b = 116.8 β = 90
c = 47.7 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2006-11-17
Diffraction Radiation
Monochromator Protocol
Diamond (111), Ge(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3

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
1.7 36.94 99.9 0.112 0.112 -- 7.0 16226 16226 0.0 0.0 --
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)
1.7 1.8 100.0 0.258 0.258 5.0 7.0 2509

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 1.7 26.01 0.0 0.0 15399 15399 811 99.96 0.1656 0.1656 0.1641 0.19396 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 1.7 1.744 -- 59 1117 0.164 0.244 -- 99.92
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 13.535
Anisotropic B[1][1] -0.66
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.53
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.13
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.598
r_scbond_it 3.093
r_mcangle_it 3.404
r_mcbond_it 2.367
r_bond_refined_d 0.012
r_angle_refined_deg 1.292
r_dihedral_angle_1_deg 5.145
r_dihedral_angle_2_deg 38.738
r_dihedral_angle_3_deg 13.63
r_chiral_restr 0.103
r_gen_planes_refined 0.005
r_nbd_refined 0.232
r_nbtor_refined 0.311
r_xyhbond_nbd_refined 0.198
r_symmetry_vdw_refined 0.187
r_symmetry_hbond_refined 0.209
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 988
Nucleic Acid Atoms 0
Heterogen Atoms 44
Solvent Atoms 155

Software

Computing
Computing Package Purpose
ProDC Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
Molrep Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement