X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details Magnesium sulfate, Sodium chloride, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.27 α = 90
b = 124.48 β = 90
c = 166.82 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
CCD ADSC QUANTUM 4 -- 2001-03-22
Diffraction Radiation
Monochromator Protocol
FIXED-EXIT DOUBLE CRYSTAL MONOCHROMATOR SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL40B2 0.9797 SPring-8 BL40B2

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
2.5 43.5 98.1 0.093 0.093 -- 4.5 46950 46835 0.0 0.0 42.9
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)
2.5 2.64 73.9 0.389 0.389 1.8 3.1 284

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 2.5 50.0 -- 0.0 47875 44422 2374 97.75 0.22545 0.22545 0.22218 0.28616 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 2.5 2.565 -- 138 2848 0.328 0.409 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.719
Anisotropic B[1][1] 0.33
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.72
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.05
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.078
r_symmetry_vdw_refined 0.181
r_bond_other_d 0.002
r_symmetry_vdw_other 0.25
r_xyhbond_nbd_refined 0.166
r_angle_refined_deg 1.441
r_bond_refined_d 0.014
r_gen_planes_other 0.002
r_gen_planes_refined 0.005
r_nbd_refined 0.198
r_scangle_it 2.82
r_dihedral_angle_1_deg 6.787
r_symmetry_hbond_refined 0.165
r_mcbond_it 0.624
r_angle_other_deg 0.819
r_mcangle_it 1.177
r_scbond_it 1.568
r_nbd_other 0.221
r_nbtor_other 0.086
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.332
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8982
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 115

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling
AMoRE phasing
REFMAC refinement version: 5.1.19
CCP4 data scaling version: (SCALA)