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_nbtor_other 0.086
r_nbd_other 0.221
r_nbd_refined 0.198
r_gen_planes_other 0.002
r_gen_planes_refined 0.005
r_chiral_restr 0.078
r_dihedral_angle_1_deg 6.787
r_angle_other_deg 0.819
r_angle_refined_deg 1.441
r_bond_other_d 0.002
r_bond_refined_d 0.014
r_xyhbond_nbd_refined 0.166
r_symmetry_vdw_refined 0.181
r_symmetry_vdw_other 0.25
r_symmetry_hbond_refined 0.165
r_mcbond_it 0.624
r_mcangle_it 1.177
r_scbond_it 1.568
r_scangle_it 2.82
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

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.19 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.19 refinement
AMoRE model building
SCALA data reduction
MOSFLM data collection