X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 1.6M ammonium formate, 100 mM Na Hepes buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.57 α = 113.25
b = 63.19 β = 100.82
c = 55.33 γ = 92.66
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS II OSMIC CONFOCAL OPTICS 2003-06-23
Diffraction Radiation
Monochromator Protocol
OSMIC CONFOCAL OPTICS SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.5418 -- --

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
2.3 57.7 94.9 0.073 -- -- 2.9 29907 28396 -- 0.0 46.6
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)
2.3 2.4 89.5 0.26 -- 1.9 -- --

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 2.3 57.74 -- 0.0 29907 26965 1431 94.95 -- 0.20828 0.20624 0.2468 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 2.3 2.36 1885 96 1885 0.333 0.412 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model TLS with each monomer comprising a separate TLS group
Mean Isotropic B 37.308
Anisotropic B[1][1] -0.52
Anisotropic B[1][2] -0.65
Anisotropic B[1][3] -0.02
Anisotropic B[2][2] 1.3
Anisotropic B[2][3] 1.68
Anisotropic B[3][3] 0.48
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.119
r_mcbond_it 0.376
r_scbond_it 0.948
r_angle_refined_deg 1.323
r_bond_refined_d 0.008
r_gen_planes_refined 0.003
r_dihedral_angle_1_deg 4.779
r_symmetry_hbond_refined 0.253
r_nbd_refined 0.207
r_symmetry_vdw_refined 0.186
r_chiral_restr 0.132
r_mcangle_it 0.69
r_scangle_it 1.688
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.317
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4857
Nucleic Acid Atoms 0
Heterogen Atoms 122
Solvent Atoms 193

Software

Software
Software Name Purpose
bioteX data collection
REFMAC refinement version: 5.1.24
bioteX data reduction
bioteX data scaling
CNS phasing