X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8.5
Temperature 294.0
Details 100mM Tris-HCl pH 8.5, 25% PEG 3350, 200mM Magnesium chloride, VAPOR DIFFUSION, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 136.38 α = 90
b = 136.38 β = 90
c = 80.93 γ = 90
Symmetry
Space Group P 4 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2007-04-08
Diffraction Radiation
Monochromator Protocol
diamond SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 31-ID 0.97958 APS 31-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
1.72 96.44 98.9 0.086 0.086 -- 12.0 81085 81085 0.0 0.0 17.8
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)
1.72 1.81 93.0 0.306 0.306 6.1 10.9 10981

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
SAD 1.72 20.0 0.0 0.0 81006 81006 4061 99.7 -- 0.167 0.165 0.191 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 1.72 1.76 5709 293 5416 0.185 0.233 -- 96.52
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.922
Anisotropic B[1][1] 0.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.04
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.319
r_scbond_it 2.364
r_mcangle_it 1.338
r_mcbond_other 0.22
r_mcbond_it 1.154
r_symmetry_hbond_refined 0.16
r_symmetry_vdw_other 0.356
r_symmetry_vdw_refined 0.315
r_xyhbond_nbd_refined 0.144
r_nbtor_other 0.086
r_nbtor_refined 0.177
r_nbd_other 0.204
r_bond_refined_d 0.012
r_bond_other_d 0.002
r_angle_refined_deg 1.341
r_angle_other_deg 0.902
r_dihedral_angle_1_deg 7.483
r_dihedral_angle_2_deg 31.606
r_dihedral_angle_3_deg 11.735
r_dihedral_angle_4_deg 16.782
r_chiral_restr 0.081
r_gen_planes_refined 0.006
r_gen_planes_other 0.001
r_nbd_refined 0.222
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5626
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 687

Software

Computing
Computing Package Purpose
MAR CCD Data Collection
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
SHELXC, SHELXD, SHELXE Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 2.000 data extraction
REFMAC5 refinement
SCALA data processing