X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

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_dihedral_angle_2_deg 36.979
r_symmetry_hbond_refined 0.095
r_gen_planes_refined 0.008
r_nbd_refined 0.216
r_dihedral_angle_3_deg 15.147
r_xyhbond_nbd_refined 0.137
r_angle_refined_deg 2.46
r_nbtor_refined 0.31
r_scangle_it 3.93
r_symmetry_vdw_refined 0.239
r_mcbond_it 1.412
r_dihedral_angle_4_deg 17.969
r_chiral_restr 0.28
r_mcangle_it 2.151
r_bond_refined_d 0.018
r_scbond_it 2.818
r_dihedral_angle_1_deg 7.599
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3394
Nucleic Acid Atoms 609
Heterogen Atoms 34
Solvent Atoms 158

Software

Software
Software Name Purpose
HKL data processing
REFMAC refinement version: 5.3.0020
PDB_EXTRACT data extraction version: 3.005
HKL data reduction
HKL data scaling