X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Dialysis
pH 7
Temperature 277.0
Details MPD, pH 7.0, Dialysis, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 44.2 α = 78.96
b = 51.05 β = 75.47
c = 93.23 γ = 70.24
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 IV confocal osmic 2001-03-28
Diffraction Radiation
Monochromator Protocol
-- 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
1.47 20 88.8 0.054 0.054 -- 2.1 156075 109109 0.0 0.0 --
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)
1.47 1.508 69.0 0.127 0.127 4.1 -- 5097

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 1.47 20.0 0.0 0.0 156075 109109 2234 88.8 0.1515 0.151 0.151 0.1831 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 1.47 1.508 5097 93 5097 0.373 0.45 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.152
Anisotropic B[1][1] -0.25
Anisotropic B[1][2] -0.02
Anisotropic B[1][3] 0.78
Anisotropic B[2][2] -0.21
Anisotropic B[2][3] 0.04
Anisotropic B[3][3] 0.06
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 7.943
r_sphericity_free 9.496
r_rigid_bond_restr 1.376
r_scangle_it 5.258
r_scbond_it 3.604
r_mcangle_it 2.276
r_mcbond_it 1.513
r_symmetry_hbond_refined 0.112
r_symmetry_vdw_other 0.308
r_symmetry_vdw_refined 0.217
r_bond_refined_d 0.016
r_bond_other_d 0.0
r_angle_refined_deg 1.634
r_angle_other_deg 3.608
r_dihedral_angle_1_deg 6.051
r_chiral_restr 0.106
r_gen_planes_refined 0.006
r_gen_planes_other 0.008
r_nbd_refined 0.233
r_nbd_other 0.288
r_nbtor_other 0.106
r_xyhbond_nbd_refined 0.094
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.042
Luzzati ESD (R-Free Set) 0.068
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5570
Nucleic Acid Atoms 0
Heterogen Atoms 112
Solvent Atoms 581

Software

Computing
Computing Package Purpose
D*TREK Data Reduction (intensity integration)
D*TREK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.27 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.27 refinement
AMoRE model building
d*trek data reduction
d*trek data collection