X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 291.0
Details PROTEIN: 12MG/ML IN 50MM MOPS PH 6.5, 50MM NACL, 1MM DTT RESERVOIR: 25% PEG 5000 MME, 0.1M TRIS PH 7.5, 0.15M MGCL2, 15% GLYCEROL TEMP: 18 DEGREES C SITTING DROP: 2 UL PROTEIN, 0.6 UL RESERVOIR

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.12 α = 90
b = 53.54 β = 110.9
c = 61.51 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 RIGAKU-MSC MIRRORS 2005-11-22
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 -- -- --

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
1.65 100 85.2 0.07 -- -- 3.3 -- 28794 -- 2.0 17.8
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)
1.65 1.71 27.5 0.36 -- 2.0 1.96 --

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 1.65 57.45 -- -- -- 27330 1464 85.17 -- 0.17267 0.17069 0.2102 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 1.65 1.693 -- 31 574 0.269 0.284 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.122
Anisotropic B[1][1] -0.23
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.53
Anisotropic B[2][2] -0.12
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.04
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 5.485
r_gen_planes_other 0.001
r_nbtor_refined 0.186
r_bond_refined_d 0.013
r_dihedral_angle_4_deg 14.609
r_symmetry_hbond_refined 0.168
r_gen_planes_refined 0.006
r_symmetry_vdw_refined 0.091
r_scbond_it 2.17
r_nbtor_other 0.08
r_dihedral_angle_3_deg 12.041
r_angle_refined_deg 1.469
r_nbd_refined 0.215
r_scangle_it 3.149
r_mcangle_it 1.348
r_mcbond_it 0.972
r_nbd_other 0.177
r_angle_other_deg 0.812
r_symmetry_vdw_other 0.259
r_bond_other_d 0.001
r_xyhbond_nbd_refined 0.166
r_dihedral_angle_2_deg 36.594
r_chiral_restr 0.088
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2123
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 260

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
CrystalClear data reduction
CrystalClear data scaling
AMoRE phasing