X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details MPD, PEG6000, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 85.11 α = 90
b = 85.11 β = 90
c = 59 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 4 -- 2001-10-19
Diffraction Radiation
Monochromator Protocol
SI (111) + GE (220) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-18B 0.9500, 0.9806, 0.9808, 1.0 Photon Factory BL-18B

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
2.1 30 100.0 0.045 -- -- -- 9302 9301 -- -- --
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)
2.1 2.21 99.6 0.267 -- 2.8 -- --

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
MAD 2.1 30.0 -- 0.0 9301 8858 443 100.0 0.2468 0.2468 0.24477 0.28951 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 2.1 2.154 -- 35 673 0.263 0.319 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 46.589
Anisotropic B[1][1] 0.09
Anisotropic B[1][2] 0.04
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.09
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.13
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.244
r_mcbond_it 1.159
r_bond_refined_d 0.017
r_dihedral_angle_3_deg 17.844
r_nbd_refined 0.281
r_mcangle_it 2.128
r_xyhbond_nbd_refined 0.274
r_chiral_restr 0.126
r_scbond_it 3.127
r_angle_refined_deg 1.727
r_scangle_it 5.374
r_dihedral_angle_1_deg 3.426
r_symmetry_vdw_refined 0.27
r_gen_planes_refined 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 886
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 108

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling
SOLVE phasing
RESOLVE model building
REFMAC refinement version: 5.0
CCP4 data scaling version: (SCALA)
RESOLVE phasing