X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 293.0
Details Sodium malonate, sodium benzoate, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 154.16 α = 90
b = 154.16 β = 90
c = 104.56 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH MIRRORS 2002-12-06
Diffraction Radiation
Monochromator Protocol
MIRRORS SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.2 -- BESSY 14.2

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
1.9 20 98.4 0.081 0.081 -- 6.8 -- 110385 -- 0.0 29.8
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)
1.9 1.92 94.4 0.55 0.55 2.3 -- --

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
SAD 1.9 20.0 -- -- 110333 104822 5511 98.2 -- -- 0.185 0.216 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 1.9 1.95 -- 369 7101 0.242 0.292 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 20.6
Anisotropic B[1][1] -1.24
Anisotropic B[1][2] -0.62
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.24
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.86
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.692
r_scbond_it 2.24
r_mcangle_it 1.627
r_mcbond_it 0.915
r_symmetry_hbond_refined 0.21
r_symmetry_vdw_other 0.242
r_symmetry_vdw_refined 0.181
r_xyhbond_nbd_other 0.121
r_xyhbond_nbd_refined 0.159
r_bond_refined_d 0.013
r_bond_other_d 0.002
r_angle_refined_deg 1.542
r_angle_other_deg 1.467
r_dihedral_angle_1_deg 15.097
r_dihedral_angle_3_deg 16.46
r_chiral_restr 0.094
r_gen_planes_refined 0.007
r_gen_planes_other 0.005
r_nbd_refined 0.298
r_nbd_other 0.218
r_nbtor_other 0.316
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8981
Nucleic Acid Atoms 0
Heterogen Atoms 117
Solvent Atoms 443

Software

Computing
Computing Package Purpose
MAR Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SHAKE-N-BAKE, SOLVE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement