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 (QUANTUM 315R) ADSC 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_scangle_it 3.113
r_scbond_it 1.842
r_mcangle_it 1.134
r_mcbond_it 0.565
r_nbd_refined 0.211
r_gen_planes_refined 0.004
r_chiral_restr 0.083
r_dihedral_angle_4_deg 17.626
r_dihedral_angle_3_deg 16.875
r_dihedral_angle_2_deg 39.311
r_dihedral_angle_1_deg 4.768
r_angle_refined_deg 1.202
r_bond_refined_d 0.011
r_nbtor_refined 0.305
r_xyhbond_nbd_refined 0.158
r_metal_ion_refined 0.119
r_symmetry_vdw_refined 0.194
r_symmetry_hbond_refined 0.186
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

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0109 refinement
PHASER model building