X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.9
Temperature 298.0
Details 0.1 M Tris-HCl pH 7.9, 0.2 M LiSO4, 19% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.98 α = 90
b = 114.1 β = 90
c = 219.28 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2008-04-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 0.9000 APS 23-ID-B

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
2.3 40 97.8 0.091 -- -- 3.4 -- 75994 -- -- --
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)
2.3 2.38 95.9 0.566 -- -- 2.4 7349

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 2.41 39.53 -- 0.0 -- 65388 3306 97.0 -- 0.188 0.186 0.236 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 2.41 2.48 -- 199 3871 0.245 0.316 -- 82.71
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 46.798
Anisotropic B[1][1] 0.44
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.41
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.02
RMS Deviations
Key Refinement Restraint Deviation
r_metal_ion_refined 0.083
r_mcangle_it 0.761
r_dihedral_angle_3_deg 18.579
r_scbond_it 1.108
r_xyhbond_nbd_refined 0.141
r_symmetry_hbond_refined 0.139
r_nbtor_refined 0.304
r_mcbond_it 0.436
r_bond_refined_d 0.009
r_dihedral_angle_1_deg 5.822
r_nbd_refined 0.195
r_dihedral_angle_4_deg 20.336
r_symmetry_vdw_refined 0.198
r_scangle_it 1.795
r_angle_refined_deg 1.231
r_gen_planes_refined 0.004
r_dihedral_angle_2_deg 37.767
r_chiral_restr 0.088
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11328
Nucleic Acid Atoms 0
Heterogen Atoms 90
Solvent Atoms 360

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 3.005
MAR345 data collection version: CCD