X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 6.9
Temperature 282.0
Details PEG 8000, HEPES, dioxane, magnesium chloride, 2-mercaptoethanol, pH 6.9, VAPOR DIFFUSION, temperature 282K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.58 α = 90
b = 73.34 β = 90
c = 48.04 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-06-19
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X9B 0.9671 NSLS X9B

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
1.55 30 97.3 -- 0.036 -- 5.0 -- 30966 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)
1.55 1.61 84.6 -- 0.28 5.4 -- --

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 1.55 48.0 -- 0.0 -- 29355 1562 97.35 -- 0.16251 0.16101 0.19023 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 1.55 1.59 -- 93 1832 0.157 0.191 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.907
Anisotropic B[1][1] -0.9
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.25
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.65
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 5.096
r_nbd_refined 0.236
r_rigid_bond_restr 1.708
r_bond_other_d 0.0
r_xyhbond_nbd_other 0.266
r_mcangle_it 3.947
r_bond_refined_d 0.006
r_dihedral_angle_3_deg 15.687
r_angle_other_deg 1.247
r_nbd_other 0.189
r_scbond_it 3.489
r_symmetry_hbond_refined 0.171
r_sphericity_free 3.578
r_gen_planes_refined 0.005
r_symmetry_vdw_refined 0.248
r_xyhbond_nbd_refined 0.189
r_scangle_it 5.293
r_sphericity_bonded 2.884
r_symmetry_vdw_other 0.173
r_angle_refined_deg 2.343
r_mcbond_it 2.697
r_gen_planes_other 0.002
r_chiral_restr 0.105
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1386
Nucleic Acid Atoms 0
Heterogen Atoms 46
Solvent Atoms 210

Software

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