X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.0
Details ammonium sulfate, MES, cobaltous (II) chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 44.93 α = 90
b = 64.52 β = 90
c = 78.82 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 113
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV mirrors 2002-09-26
Diffraction Radiation
Monochromator Protocol
Yale mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200H 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
2.25 20 89.7 0.089 -- -- 8.0 11408 10221 0.0 -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)
2.25 2.33 60.3 0.316 -- 3.1 -- 663

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 2.25 20.0 -- 0.0 10221 9642 540 89.77 0.19688 0.19688 0.1927 0.2675 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 2.25 2.308 -- 28 402 0.244 0.343 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.781
Anisotropic B[1][1] -2.63
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.89
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.26
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.325
r_scbond_it 2.707
r_mcangle_it 1.649
r_mcbond_it 0.932
r_symmetry_hbond_refined 0.263
r_symmetry_vdw_other 0.287
r_symmetry_vdw_refined 0.311
r_bond_refined_d 0.022
r_bond_other_d 0.002
r_angle_refined_deg 1.805
r_angle_other_deg 1.567
r_dihedral_angle_1_deg 6.745
r_chiral_restr 0.104
r_gen_planes_refined 0.008
r_gen_planes_other 0.006
r_nbd_refined 0.209
r_nbd_other 0.255
r_nbtor_other 0.088
r_xyhbond_nbd_refined 0.201
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2124
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 90

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement