X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details PEG8000, magnesium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.55 α = 90
b = 88.57 β = 93.72
c = 120.09 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 120
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 2000-06-03
Diffraction Radiation
Monochromator Protocol
Si(III) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MAX II BEAMLINE I711 1.018 MAX II I711

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
2.9 20 86.4 -- 0.13 -- 2.3 46919 46919 0.0 0.0 43.1
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)
2.9 2.95 62.2 -- 0.242 3.5 2.06 733

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 2.95 19.92 -- 0.0 18616 18616 986 100.0 0.2319 0.23195 0.22904 0.2868 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 2.95 3.025 -- 51 1021 0.291 0.392 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model TLS
Mean Isotropic B 26.531
Anisotropic B[1][1] -1.47
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 4.55
Anisotropic B[2][2] -7.69
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 9.75
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.307
r_gen_planes_refined 0.006
r_chiral_restr 0.107
r_dihedral_angle_3_deg 19.087
r_dihedral_angle_1_deg 2.822
r_angle_refined_deg 1.761
r_bond_refined_d 0.018
r_xyhbond_nbd_refined 0.167
r_symmetry_vdw_refined 0.298
r_symmetry_hbond_refined 0.401
r_mcbond_it 0.935
r_mcangle_it 1.792
r_scbond_it 2.158
r_scangle_it 3.699
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6260
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 84

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
REFMAC version: 5.0 refinement
AMoRE model building
SCALEPACK data reduction
DENZO data collection