X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details 18% ethylene glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.09 α = 78.49
b = 63.26 β = 88.33
c = 74.22 γ = 90
Symmetry
Space Group P 1

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate Multilayer Optic (Rigaku) 2006-11-23
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 1.54170 -- --

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
2.48 52.63 93.6 0.095 0.095 -- 2.2 26558 24859 -- -- 42.1
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)
2.48 2.61 91.9 0.425 0.425 1.8 2.1 3559

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 2.48 52.63 -- 0.0 -- 24836 1268 93.56 -- 0.225 0.221 0.286 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 2.48 2.544 1781 97 1684 0.283 0.376 -- 92.71
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.425
Anisotropic B[1][1] 0.17
Anisotropic B[1][2] 0.22
Anisotropic B[1][3] -0.33
Anisotropic B[2][2] -1.07
Anisotropic B[2][3] 0.58
Anisotropic B[3][3] 0.69
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 2.359
r_symmetry_vdw_refined 0.237
r_dihedral_angle_3_deg 19.401
r_mcbond_it 1.106
r_xyhbond_nbd_refined 0.192
r_dihedral_angle_2_deg 39.618
r_chiral_restr 0.125
r_dihedral_angle_4_deg 17.726
r_angle_refined_deg 1.932
r_nbtor_refined 0.323
r_gen_planes_refined 0.007
r_symmetry_hbond_refined 0.317
r_mcangle_it 1.759
r_dihedral_angle_1_deg 12.686
r_bond_refined_d 0.019
r_nbd_refined 0.248
r_scangle_it 3.702
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3895
Nucleic Acid Atoms 0
Heterogen Atoms 46
Solvent Atoms 63

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling version: 3.2.5
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.005
MAR345dtb data collection