X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 277.0
Details 2.6 M ammonium sulfate, 0.1 M sodium acetate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 31.91 α = 90
b = 46.25 β = 90
c = 52.65 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm mirrors 2002-03-08
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05 MPG/DESY, HAMBURG BW6

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
1.88 14.74 100.0 0.114 -- -- 7.0 6614 6611 -- 2.0 18.27
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)
1.88 1.91 99.1 0.471 -- 2.8 6.8 320

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 1.88 14.74 -- -- 6356 6258 311 98.46 -- 0.15815 0.15391 0.24784 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 1.88 1.93 356 11 356 0.203 0.286 -- 78.09
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 20.915
Anisotropic B[1][1] -1.77
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.17
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.6
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 6.437
r_bond_refined_d 0.023
r_angle_refined_deg 2.008
r_mcbond_it 1.269
r_mcangle_it 1.931
r_metal_ion_refined 0.027
r_chiral_restr 0.132
r_nbd_refined 0.233
r_nbtor_refined 0.316
r_xyhbond_nbd_refined 0.207
r_gen_planes_refined 0.01
r_symmetry_vdw_refined 0.222
r_symmetry_hbond_refined 0.171
r_dihedral_angle_2_deg 28.905
r_scbond_it 3.432
r_dihedral_angle_3_deg 16.612
r_scangle_it 5.059
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 737
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 99

Software

Software
Software Name Purpose
MAR345 data collection
MOLREP phasing
REFMAC refinement version: 5.2.0019
DENZO data reduction
SCALEPACK data scaling