X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 298.0
Details 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.81 α = 90
b = 82.03 β = 109.04
c = 58.52 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2007-02-03
Diffraction Radiation
Monochromator Protocol
single crystal Si(111) bent monochromator (horizontal focusing) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.97946 SSRL BL11-1

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 15 95.4 0.046 0.046 -- 4.7 -- 48276 0.0 0.0 30.73
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 1.86 82.1 0.176 0.176 6.57 3.4 3762

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
-- 1.72 9.91 0.0 0.0 48124 48124 2446 91.58 -- 0.18 0.178 0.221 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 1.764 2157 105 2052 0.223 0.316 -- 56.55
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 17.541
Anisotropic B[1][1] -0.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.02
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.04
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_other 0.241
r_scangle_it 3.65
r_dihedral_angle_1_deg 8.04
r_nbd_refined 0.238
r_mcangle_it 1.508
r_bond_other_d 0.002
r_angle_refined_deg 1.489
r_chiral_restr 0.151
r_nbd_other 0.211
r_symmetry_hbond_refined 0.383
r_gen_planes_other 0.001
r_dihedral_angle_4_deg 23.794
r_nbtor_other 0.112
r_scbond_it 2.504
r_dihedral_angle_2_deg 38.345
r_symmetry_vdw_refined 0.533
r_mcbond_it 0.991
r_dihedral_angle_3_deg 15.49
r_bond_refined_d 0.014
r_angle_other_deg 0.993
r_nbtor_refined 0.183
r_symmetry_vdw_other 0.334
r_gen_planes_refined 0.006
r_xyhbond_nbd_refined 0.188
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3816
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 422

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 3.000
HKL-2000 data collection
HKL-2000 data reduction
PHASER phasing