X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 4.5
Temperature 292.0
Details 0.1 M NaAcetate, 3 M NaCl,0.01 M spermidine, pH 4.5, VAPOR DIFFUSION, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 105.27 α = 90
b = 105.27 β = 90
c = 120.98 γ = 90
Symmetry
Space Group P 4

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD Monochromator (horizontally side diffracting Silicon 111 crystal) 2011-11-09
Diffraction Radiation
Monochromator Protocol
horizontally diffracting monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-2 0.87 ESRF ID23-2

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
1.99 40.3 100.0 0.11 -- -- 5.1 90469 85910 2.0 2.0 29.0
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)
1.99 2.1 100.0 0.8 -- 2.0 5.0 13179

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 1.99 40.3 2.0 2.0 90469 85910 4534 99.95 -- 0.17805 0.17602 0.21679 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 1.988 2.04 -- 334 6324 0.292 0.319 -- 99.95
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.736
Anisotropic B[1][1] 0.9
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.9
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.8
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 6.533
r_dihedral_angle_2_deg 32.334
r_mcangle_it 2.16
r_bond_refined_d 0.029
r_scbond_it 3.641
r_dihedral_angle_4_deg 20.096
r_chiral_restr 0.163
r_mcbond_it 1.306
r_angle_refined_deg 2.193
r_dihedral_angle_3_deg 16.412
r_gen_planes_refined 0.013
r_scangle_it 5.658
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7418
Nucleic Acid Atoms 0
Heterogen Atoms 34
Solvent Atoms 608

Software

Software
Software Name Purpose
DNA data collection
MOLREP phasing
REFMAC refinement version: 5.5.0109
MOSFLM data reduction
SCALA data scaling