X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details 25.5% PEG 2000 MME, 0.36 M MgCl2, 0.5 mM MnCl2, 5 mM DTT, 2 mM 3',5'-ADP, 0.1 M Tris-Cl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.76 α = 107.8
b = 118.43 β = 98.36
c = 122.38 γ = 91.4
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2005-11-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 8-BM 0.9790 APS 8-BM

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
2.34 17.95 92.7 0.074 -- -- 3.9 -- 117653 -- -- --
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)
2.34 2.42 69.6 0.372 -- 2.8 3.0 8815

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 2.35 17.95 -- 0.0 -- 100806 5045 82.3 -- 0.227 0.223 0.286 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 2.35 2.41 4332 181 4151 0.283 0.335 -- 48.7
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 54.291
Anisotropic B[1][1] -0.29
Anisotropic B[1][2] -0.16
Anisotropic B[1][3] -0.24
Anisotropic B[2][2] -0.3
Anisotropic B[2][3] -0.59
Anisotropic B[3][3] 0.16
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.683
r_scbond_it 2.415
r_mcangle_it 1.565
r_mcbond_it 1.021
r_symmetry_hbond_refined 0.181
r_bond_refined_d 0.017
r_angle_refined_deg 1.564
r_dihedral_angle_1_deg 6.405
r_dihedral_angle_2_deg 35.222
r_dihedral_angle_3_deg 17.61
r_dihedral_angle_4_deg 21.067
r_chiral_restr 0.097
r_gen_planes_refined 0.006
r_nbd_refined 0.232
r_nbtor_refined 0.311
r_xyhbond_nbd_refined 0.173
r_symmetry_vdw_refined 0.216
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19529
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 287

Software

Computing
Computing Package Purpose
ADSC QUANTUM Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
SHAKE-N-BAKE Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 2.000 data extraction
REFMAC5 version: 5.2.0019 refinement