X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details 0.1 M Magnesium formate dihydrate, 15% w/v Polyethylene glycol 3,350, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 120.8 α = 90
b = 120.8 β = 90
c = 97.35 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 92 -- 2008-05-12
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.5418 -- --

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
2.8 29.3 100.0 -- 0.184 -- 11.94 -- 18310 -- -- --
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)
2.8 2.9 100.0 -- 0.573 3.5 12.04 --

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 2.8 29.3 -- -- -- 17372 934 99.97 -- 0.22569 0.22359 0.26553 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 2.8 2.872 -- 70 1258 0.291 0.32 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.663
Anisotropic B[1][1] 0.36
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.36
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.72
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.346
r_scbond_it 1.383
r_mcangle_it 1.18
r_mcbond_it 0.654
r_nbd_refined 0.217
r_gen_planes_refined 0.004
r_chiral_restr 0.081
r_dihedral_angle_4_deg 20.433
r_dihedral_angle_3_deg 20.256
r_dihedral_angle_2_deg 38.686
r_dihedral_angle_1_deg 6.144
r_angle_refined_deg 1.355
r_bond_refined_d 0.011
r_nbtor_refined 0.306
r_xyhbond_nbd_refined 0.147
r_metal_ion_refined 0.109
r_symmetry_vdw_refined 0.155
r_symmetry_hbond_refined 0.139
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3148
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 24

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
d*TREK Data Reduction (intensity integration)
d*TREK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.006 data extraction
REFMAC5 version: 5.2.0019 refinement
Phaser molecular replacement
D*trek data processing
D*trek collection/data indexing