X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 294.0
Details PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 38.44 α = 90
b = 113.24 β = 100.53
c = 67.01 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 ADSC QUANTUM 4 -- 1997-07-15
Diffraction Radiation
Monochromator Protocol
Double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12C 1.0 NSLS X12C

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 38 83.0 0.063 0.063 -- 2.8 38057 31588 -3.0 -3.0 35.4
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)
2.0 2.03 60.0 0.195 0.195 2.8 1.55 1153

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 2.0 37.8 -- -3.0 -- 28437 3125 82.95 0.20128 0.201 0.19506 0.25934 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 2.0 2.052 -- 169 1575 0.213 0.277 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 29.841
Anisotropic B[1][1] -1.95
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.4
Anisotropic B[2][2] 3.71
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.91
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.86
r_scbond_it 2.723
r_mcangle_it 3.824
r_mcbond_it 2.687
r_symmetry_hbond_other 0.141
r_symmetry_hbond_refined 0.256
r_symmetry_vdw_other 0.162
r_symmetry_vdw_refined 0.184
r_xyhbond_nbd_other 0.027
r_xyhbond_nbd_refined 0.173
r_bond_refined_d 0.018
r_bond_other_d 0.001
r_angle_refined_deg 2.704
r_angle_other_deg 1.634
r_dihedral_angle_1_deg 5.066
r_dihedral_angle_3_deg 19.12
r_chiral_restr 0.162
r_gen_planes_refined 0.015
r_gen_planes_other 0.007
r_nbd_refined 0.219
r_nbd_other 0.162
r_nbtor_other 0.031
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4712
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 144

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
X-PLOR Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
X-PLOR model building
SCALEPACK data reduction
DENZO data collection