X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 291.0
Details 15% acetone, 0.6M Ammonium formate (metal basis), 0.6M sodium citrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 82.46 α = 90
b = 82.46 β = 90
c = 33.84 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 291
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate -- 2008-06-20
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.5418 -- --

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
2.56 14.75 -- -- 0.103 -- -- 2464 2479 -- -- --
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)
2.56 2.64 -- -- -- 4.3 -- --

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 2.56 14.75 -- -- -- 2468 283 99.14 -- 0.20007 0.19788 0.21956 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 2.555 2.62 -- 22 191 0.231 0.276 -- 99.53
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.369
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.216
r_mcangle_it 1.038
r_mcbond_it 0.56
r_dihedral_angle_2_deg 38.51
r_symmetry_metal_ion_refined 0.002
r_scangle_it 1.817
r_gen_planes_refined 0.004
r_scbond_it 1.154
r_xyhbond_nbd_refined 0.34
r_nbtor_refined 0.306
r_bond_refined_d 0.011
r_dihedral_angle_3_deg 17.972
r_dihedral_angle_1_deg 5.957
r_symmetry_vdw_refined 0.206
r_chiral_restr 0.087
r_nbd_refined 0.274
r_dihedral_angle_4_deg 6.291
r_angle_refined_deg 1.227
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 800
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 35

Software

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