X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Under Oil Microbatch
Temperature 277.0
Details Magnesium Formate, PEG 3350, Xylitol, under oil microbatch, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.45 α = 90
b = 93.14 β = 90
c = 112.57 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD -- -- 2008-01-01
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
2 30 99.1 0.055 -- -- 5.5 -- 44865 -- -- --
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)
2.0 2.07 100.0 0.337 -- -- 5.6 --

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
MOLECULAR REPLACEMENT 2.0 24.8 -- -- -- 42562 2258 98.25 -- 0.19931 0.19706 0.24336 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 2.003 2.054 -- 148 2753 0.215 0.305 -- 87.94
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.379
Anisotropic B[1][1] -0.04
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.04
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.93
r_scbond_it 2.818
r_mcangle_it 2.151
r_mcbond_it 1.412
r_nbd_refined 0.216
r_gen_planes_refined 0.008
r_chiral_restr 0.28
r_dihedral_angle_4_deg 17.969
r_dihedral_angle_3_deg 15.147
r_dihedral_angle_2_deg 36.979
r_dihedral_angle_1_deg 7.599
r_angle_refined_deg 2.46
r_bond_refined_d 0.018
r_nbtor_refined 0.31
r_xyhbond_nbd_refined 0.137
r_symmetry_vdw_refined 0.239
r_symmetry_hbond_refined 0.095
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3354
Nucleic Acid Atoms 609
Heterogen Atoms 34
Solvent Atoms 158

Software

Computing
Computing Package Purpose
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.005 data extraction
REFMAC5 version: 5.3.0020 refinement
HKL data processing