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_scangle_it 3.215
r_scbond_it 2.139
r_mcangle_it 1.524
r_mcbond_it 0.89
r_symmetry_hbond_refined 0.264
r_bond_refined_d 0.016
r_angle_refined_deg 1.782
r_dihedral_angle_1_deg 7.797
r_dihedral_angle_2_deg 36.352
r_dihedral_angle_3_deg 19.045
r_dihedral_angle_4_deg 16.392
r_chiral_restr 0.117
r_gen_planes_refined 0.006
r_nbd_refined 0.222
r_nbtor_refined 0.307
r_xyhbond_nbd_refined 0.258
r_symmetry_vdw_refined 0.238
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

Computing
Computing Package Purpose
MAR345dtb Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.2 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 2.000 data extraction
REFMAC5 refinement
SCALA data processing