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_dihedral_angle_1_deg 7.483
r_nbtor_refined 0.177
r_chiral_restr 0.081
r_gen_planes_other 0.001
r_mcangle_it 1.338
r_symmetry_vdw_refined 0.315
r_bond_refined_d 0.012
r_scangle_it 3.319
r_dihedral_angle_2_deg 31.606
r_dihedral_angle_4_deg 16.782
r_nbd_refined 0.222
r_symmetry_vdw_other 0.356
r_bond_other_d 0.002
r_angle_other_deg 0.902
r_nbtor_other 0.086
r_angle_refined_deg 1.341
r_gen_planes_refined 0.006
r_nbd_other 0.204
r_scbond_it 2.364
r_mcbond_other 0.22
r_dihedral_angle_3_deg 11.735
r_mcbond_it 1.154
r_symmetry_hbond_refined 0.16
r_xyhbond_nbd_refined 0.144
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

Software
Software Name Purpose
SCALA data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 2.000
MAR data collection version: CCD
MOSFLM data reduction
CCP4 data scaling version: (SCALA)
SHELXC phasing
SHELXD phasing
SHELXE model building