X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details 21% PEG 4000, 0.2M ammonium sulfate, 0.1M sodium citrate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.28 α = 90
b = 63.3 β = 90
c = 132.76 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 113
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ MSC Blue Confocal optics 2004-02-15
Diffraction Radiation
Monochromator Protocol
MSC BLUE CONFOCAL OPTICS SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 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
1.8 45.8 98.7 0.065 -- -- 3.7 46175 45573 -- -- --
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)
1.8 1.86 90.1 0.347 -- 3.3 3.4 4549

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 1.8 20.0 -- -- -- 42941 2296 99.38 -- 0.19533 0.19268 0.2461 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 1.8 1.897 -- 325 6126 0.263 0.306 -- 99.11
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.84
Anisotropic B[1][1] -0.26
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.39
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.13
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_refined 0.312
r_scbond_it 3.061
r_chiral_restr 0.137
r_symmetry_hbond_refined 0.16
r_bond_refined_d 0.021
r_gen_planes_refined 0.009
r_dihedral_angle_4_deg 16.75
r_mcangle_it 1.941
r_xyhbond_nbd_refined 0.181
r_angle_refined_deg 1.819
r_dihedral_angle_1_deg 7.176
r_dihedral_angle_2_deg 35.083
r_dihedral_angle_3_deg 14.85
r_nbd_refined 0.219
r_symmetry_vdw_refined 0.229
r_mcbond_it 1.292
r_scangle_it 4.628
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3333
Nucleic Acid Atoms 0
Heterogen Atoms 82
Solvent Atoms 417

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0003
CrystalClear data reduction version: (MSC/RIGAKU)
d*TREK data scaling
AMoRE phasing