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_scangle_it 1.843
r_scbond_it 1.246
r_mcangle_it 0.835
r_mcbond_it 0.465
r_symmetry_hbond_refined 0.119
r_bond_refined_d 0.011
r_angle_refined_deg 1.481
r_dihedral_angle_1_deg 6.913
r_dihedral_angle_2_deg 38.813
r_dihedral_angle_3_deg 20.076
r_dihedral_angle_4_deg 17.25
r_chiral_restr 0.093
r_gen_planes_refined 0.005
r_nbd_refined 0.213
r_nbtor_refined 0.306
r_xyhbond_nbd_refined 0.157
r_symmetry_vdw_refined 0.188
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3478
Nucleic Acid Atoms 609
Heterogen Atoms 24
Solvent Atoms 57

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.3.0020 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.004 data extraction
REFMAC5 version: 5.3.0020 refinement
Phaser molecular replacement
HKL data processing