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 1.9 M Sodium Formate, 0.1 M Bis-tris propane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 112.53 α = 90
b = 112.53 β = 90
c = 29.37 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2006-06-26
Diffraction Radiation
Monochromator Protocol
Si(311) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 1.033130 ESRF ID29

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
1.9 30 97.5 -- 0.056 -- 5.6 10665 10665 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)
1.9 2.0 88.8 -- 0.226 6.47 4.8 --

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 1.9 21.27 -- 0.0 10151 10151 510 97.52 0.179 0.17325 0.1707 0.22469 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 1.9 1.949 -- 25 625 0.194 0.244 -- 80.55
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.399
Anisotropic B[1][1] 0.05
Anisotropic B[1][2] 0.02
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.07
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.008
r_nbtor_other 0.088
r_symmetry_vdw_refined 0.144
r_scangle_it 4.285
r_angle_other_deg 1.092
r_dihedral_angle_3_deg 14.267
r_symmetry_vdw_other 0.265
r_angle_refined_deg 1.774
r_dihedral_angle_1_deg 7.258
r_symmetry_hbond_refined 0.258
r_nbtor_refined 0.186
r_bond_other_d 0.003
r_chiral_restr 0.122
r_scbond_it 3.21
r_nbd_refined 0.207
r_gen_planes_other 0.002
r_bond_refined_d 0.02
r_mcbond_it 1.801
r_dihedral_angle_4_deg 23.97
r_mcbond_other 0.354
r_nbd_other 0.2
r_dihedral_angle_2_deg 34.756
r_xyhbond_nbd_refined 0.206
r_mcangle_it 2.153
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 985
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 110

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
XDS data reduction
XSCALE data scaling
SHARP phasing