X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.3
Temperature 293.0
Details 3 microliters crystallization buffer (10 mM Tris/HCl, 300 mM NaCl, pH 7.3) containing the complex plus 1 microliter reservoir solution (100 mM KCl, 100 mM MgCl2, 6% isopropanol, 50 mM sodium cacodylate, pH 6.0), VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.44 α = 90
b = 68.88 β = 92.27
c = 114.35 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
CCD ADSC QUANTUM 105 ID14-2 (mirror) 2003-02-10
Diffraction Radiation
Monochromator Protocol
ID14-2 (mirror) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 -- ESRF ID14-2

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
1.6 19.66 95.8 0.117 0.117 -- 7.2 121645 116532 0.0 0.0 18.55
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)
1.6 1.65 58.6 0.34 0.34 3.58 3.92 10668

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 1.61 19.64 -- 0.0 121568 116531 5826 95.86 -- 0.16195 0.16022 0.19508 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 1.613 1.654 6974 349 6625 0.19 0.225 -- 80.08
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.678
Anisotropic B[1][1] -0.13
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.17
Anisotropic B[2][2] 0.32
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.2
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_refined 0.149
r_dihedral_angle_1_deg 6.023
r_mcangle_it 1.196
r_chiral_restr 0.086
r_dihedral_angle_3_deg 12.89
r_scangle_it 2.589
r_gen_planes_refined 0.006
r_nbtor_refined 0.311
r_xyhbond_nbd_refined 0.138
r_angle_refined_deg 1.409
r_dihedral_angle_2_deg 31.363
r_dihedral_angle_4_deg 14.224
r_bond_refined_d 0.009
r_scbond_it 1.69
r_symmetry_hbond_refined 0.147
r_mcbond_it 0.772
r_nbd_refined 0.197
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6378
Nucleic Acid Atoms 808
Heterogen Atoms 74
Solvent Atoms 1413

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
ProDC data collection
MAR345 data collection
XDS data scaling
MOLREP phasing