X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details 19% Ethylene glycol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42 α = 78.78
b = 63.02 β = 88.8
c = 73.95 γ = 90.14
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate Osmic 2006-11-11
Diffraction Radiation
Monochromator Protocol
Multilayer Optic (Rigaku) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 1.5417 -- --

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
2.32 72.55 93.8 0.075 0.075 -- 2.2 32189 30194 -- -- 38.452
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)
2.32 2.45 91.6 0.37 0.37 2.1 2.2 4326

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 2.32 72.548 -- 0.0 32189 30188 1546 93.79 0.209 0.209 0.205 0.28 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 2.32 2.38 2177 121 2056 0.247 0.295 -- 91.7
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.707
Anisotropic B[1][1] -0.31
Anisotropic B[1][2] 0.02
Anisotropic B[1][3] -0.4
Anisotropic B[2][2] -0.48
Anisotropic B[2][3] 0.76
Anisotropic B[3][3] 0.51
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.258
r_dihedral_angle_3_deg 19.045
r_chiral_restr 0.117
r_nbtor_refined 0.307
r_scangle_it 3.215
r_mcbond_it 0.89
r_symmetry_vdw_refined 0.238
r_gen_planes_refined 0.006
r_nbd_refined 0.222
r_dihedral_angle_2_deg 36.352
r_mcangle_it 1.524
r_scbond_it 2.139
r_symmetry_hbond_refined 0.264
r_bond_refined_d 0.016
r_dihedral_angle_4_deg 16.392
r_dihedral_angle_1_deg 7.797
r_angle_refined_deg 1.782
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3991
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 172

Software

Software
Software Name Purpose
SCALA data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 2.000
MAR345dtb data collection
MOSFLM data reduction
PHASER phasing