X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 9
Temperature 298.0
Details Na-Bicine 0.1M pH 9, Na-Malonate 2.2M pH 7, VAPOR DIFFUSION, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.21 α = 90
b = 41.18 β = 104.29
c = 71.92 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMosaic, 225 mm Detector swing-out angle up to 30 degrees 2010-11-14
Diffraction Radiation
Monochromator Protocol
Double crystal Si(111), horizontally focussing SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.9748 EMBL/DESY, Hamburg X12

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
1.3 41.18 95.9 0.064 0.064 -- 7.6 -- 56499 0.0 0.0 12.15
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)
1.3 1.37 93.6 0.38 0.38 2.0 7.7 8022

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
MR 1.3 39.84 0.0 0.0 56499 56478 5694 95.53 -- 0.146 0.142 0.179 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 1.3 1.334 -- 398 3642 0.217 0.298 -- 92.89
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.21
Anisotropic B[1][1] -0.56
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.54
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.02
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.015
r_rigid_bond_restr 3.305
r_scbond_it 4.992
r_nbtor_refined 0.322
r_angle_refined_deg 2.348
r_mcbond_it 2.928
r_sphericity_bonded 9.391
r_nbd_refined 0.226
r_xyhbond_nbd_refined 0.149
r_symmetry_hbond_refined 0.189
r_dihedral_angle_2_deg 35.159
r_chiral_restr 0.191
r_dihedral_angle_1_deg 6.606
r_dihedral_angle_3_deg 12.968
r_sphericity_free 15.581
r_scangle_it 6.284
r_mcangle_it 3.836
r_bond_refined_d 0.028
r_metal_ion_refined 0.083
r_dihedral_angle_4_deg 22.139
r_symmetry_vdw_refined 0.19
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2049
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 248

Software

Software
Software Name Purpose
REFMAC refinement
MOSFLM data reduction
SCALA data scaling version: 3.2.19
PDB_EXTRACT data extraction version: 3.006
MAR345 data collection version: v. 0.10.22 on RedHat Linux 8