X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details 12%PEG 400,200mM NaCl, pH 7., VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 173.42 α = 90
b = 46.13 β = 129.42
c = 129.32 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 109
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 mirrors 2006-04-06
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-ID 1 APS 17-ID

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
2.31 50 91.7 0.027 0.027 -- -- -- 30304 -3.0 -- --
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)
2.31 -- 74.8 0.055 0.055 10.8 -- --

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 2.31 50.0 -- -- -- 28772 1530 86.11 -- 0.18519 0.18101 0.26433 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 2.31 2.37 -- 28 440 0.193 0.235 -- 18.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Anisotropic
Mean Isotropic B 52.97
Anisotropic B[1][1] -2.79
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -3.39
Anisotropic B[2][2] 3.33
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.84
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.687
r_dihedral_angle_2_deg 30.318
r_nbd_refined 0.235
r_dihedral_angle_1_deg 7.509
r_mcbond_it 1.559
r_dihedral_angle_3_deg 20.234
r_symmetry_vdw_refined 0.228
r_bond_refined_d 0.022
r_mcangle_it 2.563
r_xyhbond_nbd_refined 0.181
r_chiral_restr 0.127
r_scbond_it 4.067
r_angle_refined_deg 2.448
r_gen_planes_refined 0.009
r_nbtor_refined 0.315
r_symmetry_hbond_refined 0.123
r_dihedral_angle_4_deg 21.317
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3361
Nucleic Acid Atoms 1306
Heterogen Atoms 0
Solvent Atoms 123

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 2.000
ADSC data collection version: Quantum
HKL-2000 data reduction
SCALEPACK data scaling
PHASER phasing