X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 9
Temperature 298.0
Details 20%(w/v)PEG1K, 100mM magnesium acetate, 100mM TRIS, 5mM araC, 5mM ADP, 5mM MgCl2, 5mM DTT, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.72 α = 90
b = 80.72 β = 90
c = 94.28 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2002-11-26
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID

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
1.6 30 -- -- 0.052 -- 11.8 -- 41303 -- -- 25.0
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)
1.6 1.7 -- -- 0.511 4.9 -- --

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 1.6 20.0 -- 0.0 -- 37175 4127 99.04 -- 0.1754 0.17298 0.19694 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 1.6 1.641 -- 287 2722 0.234 0.236 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.373
Anisotropic B[1][1] 1.08
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.08
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.16
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.641
r_scbond_it 2.854
r_mcangle_it 2.088
r_mcbond_it 1.151
r_symmetry_hbond_refined 0.152
r_symmetry_vdw_other 0.309
r_symmetry_vdw_refined 0.075
r_bond_refined_d 0.018
r_bond_other_d 0.002
r_angle_refined_deg 1.77
r_angle_other_deg 0.929
r_dihedral_angle_1_deg 5.204
r_chiral_restr 0.109
r_gen_planes_refined 0.011
r_gen_planes_other 0.013
r_nbd_refined 0.217
r_nbd_other 0.245
r_nbtor_other 0.083
r_xyhbond_nbd_refined 0.158
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1902
Nucleic Acid Atoms 0
Heterogen Atoms 45
Solvent Atoms 176

Software

Computing
Computing Package Purpose
XDS Data Reduction (data scaling)
SOLVE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement