X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch
pH 8.5
Temperature 295.0
Details PEG 4000, CHES, pH 8.5, microbatch, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.2 α = 90
b = 55.32 β = 90
c = 77.48 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS V RH coated bent-cylindrical mirror 2004-02-28
IMAGE PLATE RIGAKU RAXIS V -- 2004-05-29
Diffraction Radiation
Monochromator Protocol
-- MAD
SI111 double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0 SPring-8 BL26B1
SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0, 0.97946, 0.97914 SPring-8 BL26B1

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
1.85 40 98.8 0.065 -- -- 4.7 18717 18477 0.0 0.0 20.03
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)
1.85 1.92 99.8 0.277 -- -- -- --

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 1.85 27.66 -- 0.0 18717 18477 993 98.75 -- 0.219 0.219 0.259 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 1.851 1.899 -- 80 1305 0.247 0.262 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.351
Anisotropic B[1][1] -1.09
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.66
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.57
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.002
r_angle_other_deg 1.068
r_chiral_restr 0.052
r_nbtor_other 0.081
r_xyhbond_nbd_refined 0.125
r_nbd_refined 0.187
r_symmetry_vdw_other 0.299
r_scangle_it 3.019
r_symmetry_hbond_refined 0.146
r_mcangle_it 1.011
r_gen_planes_other 0.001
r_bond_refined_d 0.007
r_dihedral_angle_1_deg 4.899
r_scbond_it 1.656
r_angle_refined_deg 0.96
r_gen_planes_refined 0.003
r_nbd_other 0.219
r_mcbond_it 0.514
r_symmetry_vdw_refined 0.114
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1874
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 166

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.27
HKL-2000 data reduction
SCALEPACK data scaling
SOLVE phasing