X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.3
Temperature 293.0
Details 0.1 M sodium acetate, 12% PEG 6000, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.82 α = 90
b = 86.83 β = 90
c = 171.31 γ = 90
Symmetry
Space Group P 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 130 mm MIRRORS 2006-03-30
Diffraction Radiation
Monochromator Protocol
Silicon SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.438 LNLS D03B-MX1

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
1.98 20 93.8 0.075 0.075 -- 5.8 46352 43478 2.0 2.0 --
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)
1.98 2.09 90.1 0.302 0.302 4.3 5.3 --

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 1.98 14.94 -- -- 42925 41174 2190 95.92 -- 0.18881 0.18637 0.23377 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 1.983 2.034 -- 125 2534 0.226 0.268 -- 81.64
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 24.153
Anisotropic B[1][1] -0.11
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.1
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.208
r_scbond_it 1.702
r_metal_ion_refined 0.017
r_symmetry_vdw_refined 0.209
r_mcbond_it 0.546
r_dihedral_angle_4_deg 20.688
r_chiral_restr 0.087
r_dihedral_angle_3_deg 16.136
r_dihedral_angle_1_deg 5.501
r_dihedral_angle_2_deg 37.644
r_gen_planes_refined 0.005
r_nbtor_refined 0.304
r_bond_refined_d 0.011
r_angle_refined_deg 1.483
r_mcangle_it 0.932
r_scangle_it 2.746
r_xyhbond_nbd_refined 0.151
r_symmetry_hbond_refined 0.136
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4535
Nucleic Acid Atoms 0
Heterogen Atoms 128
Solvent Atoms 463

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
MAR345 data collection
MOSFLM data reduction
SCALA data scaling
PHASER phasing