X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details 3 M MALONATE PH7.0, 10 MM ZNCL2

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 132.89 α = 90
b = 110.62 β = 103.34
c = 97.41 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r MIRRORS 2010-07-28
Diffraction Radiation
Monochromator Protocol
SILICON MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I02 -- Diamond I02

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
2.4 29.46 97.4 0.07 -- -- 4.6 -- 52114 -- 0.0 56.6
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)
2.4 2.53 96.3 0.44 -- 3.0 4.7 --

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 2.4 94.782 -- 1.0 -- 52094 2642 97.145 -- 0.188 0.1862 0.2215 --
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 2.4 2.462 -- 203 3649 0.294 0.342 -- 97.248
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 60.064
Anisotropic B[1][1] -0.188
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.366
Anisotropic B[2][2] -0.335
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.108
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.083
r_scbond_it 1.842
r_bond_refined_d 0.011
r_mcbond_it 0.565
r_gen_planes_refined 0.004
r_nbtor_refined 0.305
r_angle_refined_deg 1.202
r_nbd_refined 0.211
r_mcangle_it 1.134
r_xyhbond_nbd_refined 0.158
r_scangle_it 3.113
r_dihedral_angle_3_deg 16.875
r_dihedral_angle_4_deg 17.626
r_symmetry_vdw_refined 0.194
r_dihedral_angle_2_deg 39.311
r_symmetry_hbond_refined 0.186
r_metal_ion_refined 0.119
r_dihedral_angle_1_deg 4.768
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5000
Nucleic Acid Atoms 0
Heterogen Atoms 35
Solvent Atoms 246

Software

Software
Software Name Purpose
REFMAC refinement version: 5.5.0109
XDS data reduction
SCALA data scaling
PHASER phasing