X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Under Oil Microbatch
pH 6
Temperature 277.0
Details Bis-Tris, MgCl2, PEG 3350, Sorbitol, pH 6.0, under oil microbatch, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 62.94 α = 90
b = 95.97 β = 90
c = 223.63 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD -- -- 2005-10-08
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X6A 1.0094 NSLS X6A

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
2.47 50 99.2 0.07 -- -- 5.9 -- 24758 -- -- --
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)
2.47 2.56 95.4 0.549 -- -- 3.8 2325

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 2.47 28.28 -- 0.0 -- 24719 1255 99.24 -- 0.232 0.23 0.277 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 2.47 2.529 -- 71 1632 0.388 0.39 -- 94.56
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 40.915
Anisotropic B[1][1] 0.16
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.19
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.03
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_refined 0.306
r_dihedral_angle_4_deg 17.25
r_mcbond_it 0.465
r_angle_refined_deg 1.481
r_symmetry_hbond_refined 0.119
r_gen_planes_refined 0.005
r_mcangle_it 0.835
r_bond_refined_d 0.011
r_symmetry_vdw_refined 0.188
r_scbond_it 1.246
r_dihedral_angle_1_deg 6.913
r_dihedral_angle_3_deg 20.076
r_scangle_it 1.843
r_dihedral_angle_2_deg 38.813
r_chiral_restr 0.093
r_xyhbond_nbd_refined 0.157
r_nbd_refined 0.213
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3489
Nucleic Acid Atoms 609
Heterogen Atoms 24
Solvent Atoms 57

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
REFMAC refinement version: 5.3.0020
PDB_EXTRACT data extraction version: 3.004
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling