X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7
Temperature 298.0
Details 2.4M Na-Malonate, pH 7, VAPOR DIFFUSION, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.01 α = 90
b = 41.06 β = 104.15
c = 71.84 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 2010-11-13
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 69.67 100.0 0.129 0.129 -- 7.0 -- 58642 0.0 0.0 10.8
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 1.37 100.0 0.368 0.368 1.6 5.8 8514

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 69.67 -- 0.0 58625 58625 5908 100.0 0.148 0.148 0.143 0.192 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 -- 433 3869 0.202 0.313 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.204
Anisotropic B[1][1] 0.58
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.6
Anisotropic B[2][2] 0.34
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.21
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 3.185
r_mcangle_it 4.035
r_sphericity_free 16.406
r_scbond_it 5.479
r_scangle_it 6.921
r_bond_refined_d 0.034
r_chiral_restr 0.203
r_dihedral_angle_1_deg 6.99
r_dihedral_angle_4_deg 21.041
r_sphericity_bonded 10.158
r_rigid_bond_restr 3.716
r_nbd_refined 0.24
r_nbtor_refined 0.321
r_metal_ion_refined 0.061
r_symmetry_hbond_refined 0.232
r_angle_refined_deg 2.641
r_gen_planes_refined 0.018
r_dihedral_angle_3_deg 13.316
r_symmetry_vdw_refined 0.233
r_dihedral_angle_2_deg 34.353
r_xyhbond_nbd_refined 0.186
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2059
Nucleic Acid Atoms 0
Heterogen Atoms 43
Solvent Atoms 304

Software

Software
Software Name Purpose
REFMAC refinement
MOSFLM data reduction
SCALA data scaling version: 3.2.19
PDB_EXTRACT data extraction version: 3.006
MAR345dtb data collection