X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Micro Batch
pH 6
Temperature 297.0
Details Sodium Malonate, MES, pH 6.0, Micro-Batch, temperature 297K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 91.48 α = 90
b = 120.9 β = 90
c = 74.32 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH Bent cylindrical Si-mirror (Rh coating) 2003-06-27
Diffraction Radiation
Monochromator Protocol
Diamond (111) double-crystal monochromator SINGLE WAVELENGTH
Diamond (111) double-crystal monochromator MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-ID-B 1.127 APS 14-ID-B
SYNCHROTRON APS BEAMLINE 14-ID-B 0.979 APS 14-ID-B

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 50 99.2 0.048 0.048 -- 7.3 32697 32697 0.0 0.0 40.5
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 1.97 98.8 0.336 0.336 5.07 6.6 3191

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
MAD 1.9 20.0 0.0 0.0 32697 30975 1654 99.28 0.191 0.19301 0.19147 0.22171 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 1.947 3191 117 2215 0.251 0.285 -- 98.8
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.419
Anisotropic B[1][1] -1.47
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.53
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.747
r_scbond_it 2.941
r_mcangle_it 2.207
r_mcbond_it 1.254
r_symmetry_hbond_refined 0.376
r_symmetry_vdw_other 0.312
r_symmetry_vdw_refined 0.197
r_bond_refined_d 0.02
r_bond_other_d 0.002
r_angle_refined_deg 1.903
r_angle_other_deg 0.948
r_dihedral_angle_1_deg 6.976
r_chiral_restr 0.116
r_gen_planes_refined 0.014
r_gen_planes_other 0.019
r_nbd_refined 0.218
r_nbd_other 0.242
r_nbtor_other 0.091
r_xyhbond_nbd_refined 0.183
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2302
Nucleic Acid Atoms 0
Heterogen Atoms 7
Solvent Atoms 214

Software

Computing
Computing Package Purpose
MAR Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SOLVE/RESOLVE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
SOLVE/RESOLVE model building
SCALEPACK data reduction
MAR data collection