X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 30 % PEG5000 MME, 0.1 M sodium acetate, 5 mM beta-mercaptoethanol, 0.1 M MES (Crystals were soaked in mother liquor containing 1 M magnesium chloride for 1 hour), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.69 α = 90
b = 45.08 β = 110.96
c = 71.79 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS -- 1999-08-08
Diffraction Radiation
Monochromator Protocol
Yale mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 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
1.9 67.42 99.5 -- -- -- -- 25897 25897 0.0 0.0 --
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)
1.9 1.949 99.5 -- -- -- -- --

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 1.9 67.42 -- 0.0 25847 25847 1306 99.43 -- 0.15845 0.1559 0.20348 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 1.9 1.949 -- 87 1824 0.243 0.345 -- 99.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 19.369
Anisotropic B[1][1] -1.74
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.42
Anisotropic B[2][2] 1.47
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.03
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.933
r_xyhbond_nbd_other 0.006
r_bond_refined_d 0.015
r_dihedral_angle_3_deg 17.566
r_mcangle_it 2.656
r_angle_other_deg 0.83
r_dihedral_angle_1_deg 6.346
r_symmetry_vdw_other 0.244
r_symmetry_hbond_refined 0.349
r_mcbond_it 1.711
r_symmetry_vdw_refined 0.247
r_angle_refined_deg 1.739
r_metal_ion_refined 0.01
r_bond_other_d 0.0
r_nbd_other 0.219
r_xyhbond_nbd_refined 0.18
r_gen_planes_refined 0.006
r_scbond_it 3.982
r_nbd_refined 0.235
r_chiral_restr 0.113
r_gen_planes_other 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2727
Nucleic Acid Atoms 0
Heterogen Atoms 35
Solvent Atoms 235

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling
REFMAC refinement version: 5.0
CCP4 data scaling version: (SCALA)