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_scangle_it 2.746
r_scbond_it 1.702
r_mcangle_it 0.932
r_mcbond_it 0.546
r_nbd_refined 0.208
r_gen_planes_refined 0.005
r_chiral_restr 0.087
r_dihedral_angle_4_deg 20.688
r_dihedral_angle_3_deg 16.136
r_dihedral_angle_2_deg 37.644
r_dihedral_angle_1_deg 5.501
r_angle_refined_deg 1.483
r_bond_refined_d 0.011
r_nbtor_refined 0.304
r_xyhbond_nbd_refined 0.151
r_metal_ion_refined 0.017
r_symmetry_vdw_refined 0.209
r_symmetry_hbond_refined 0.136
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4502
Nucleic Acid Atoms 0
Heterogen Atoms 128
Solvent Atoms 463

Software

Computing
Computing Package Purpose
MAR Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement