X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 294.0
Details 12% PEG 3000, 150 mM Li2SO4, 0.1 M imidazole, 2% ethanol, 10% ethylene glycol, 20 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.19 α = 90
b = 70.71 β = 99.14
c = 81.69 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 ADSC QUANTUM 210 -- 2008-02-16
Diffraction Radiation
Monochromator Protocol
Diamond (111), Ge(220) Sagitally focusing Ge(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.93 ESRF ID14-1

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
1.75 26.85 91.5 0.077 0.077 -- 2.9 142967 49952 -- -- 16.39
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)
1.75 1.84 89.6 0.422 -- 2.8 2.8 7129

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 1.75 26.854 -- -- 54277 47415 2526 91.28 -- 0.18711 0.18419 0.24111 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 1.75 1.795 -- 173 3446 0.271 0.32 -- 89.49
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.653
Anisotropic B[1][1] 0.55
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.3
Anisotropic B[2][2] 0.52
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.16
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.763
r_scbond_it 2.436
r_mcangle_it 1.559
r_mcbond_it 1.021
r_nbd_refined 0.212
r_gen_planes_refined 0.007
r_chiral_restr 0.105
r_dihedral_angle_4_deg 16.84
r_dihedral_angle_3_deg 15.328
r_dihedral_angle_2_deg 37.151
r_dihedral_angle_1_deg 6.033
r_angle_refined_deg 1.642
r_bond_refined_d 0.017
r_nbtor_refined 0.306
r_xyhbond_nbd_refined 0.172
r_symmetry_vdw_refined 0.195
r_symmetry_hbond_refined 0.217
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4205
Nucleic Acid Atoms 0
Heterogen Atoms 70
Solvent Atoms 565

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
AMoRE Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement
AMoRE model building
ADSC version: Quantum data collection