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_scangle_it 5.658
r_scbond_it 3.641
r_mcangle_it 2.16
r_mcbond_it 1.306
r_gen_planes_refined 0.013
r_chiral_restr 0.163
r_dihedral_angle_4_deg 20.096
r_dihedral_angle_3_deg 16.412
r_dihedral_angle_2_deg 32.334
r_dihedral_angle_1_deg 6.533
r_angle_refined_deg 2.193
r_bond_refined_d 0.029
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

Computing
Computing Package Purpose
DNA Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0109 refinement
MOLREP model building
DNA data collection