X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details 16% Ethylene glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 41.94 α = 78.28
b = 63.53 β = 90.37
c = 74.5 γ = 89.45
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 -- 2006-12-13
Diffraction Radiation
Monochromator Protocol
Multilayer Optic (Osmic) 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
2.33 72.94 90.7 0.06 0.06 -- 3.7 32156 29166 -- -- --
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)
2.33 2.46 85.9 0.407 0.407 1.8 3.6 --

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 2.33 72.93 -- -- 32683 27702 1463 90.72 -- 0.21508 0.2123 0.26673 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 2.33 2.391 -- 98 1900 0.247 0.345 -- 84.95
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.043
Anisotropic B[1][1] 0.06
Anisotropic B[1][2] -0.08
Anisotropic B[1][3] 0.17
Anisotropic B[2][2] -0.44
Anisotropic B[2][3] 0.82
Anisotropic B[3][3] 0.05
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.329
r_nbtor_refined 0.309
r_gen_planes_refined 0.006
r_dihedral_angle_4_deg 16.877
r_scbond_it 2.237
r_angle_refined_deg 1.77
r_mcbond_it 0.96
r_mcangle_it 1.642
r_xyhbond_nbd_refined 0.175
r_symmetry_vdw_refined 0.242
r_nbd_refined 0.219
r_dihedral_angle_1_deg 9.703
r_chiral_restr 0.124
r_bond_refined_d 0.016
r_dihedral_angle_2_deg 37.581
r_scangle_it 3.433
r_dihedral_angle_3_deg 17.754
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3892
Nucleic Acid Atoms 0
Heterogen Atoms 93
Solvent Atoms 99

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