X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 277.0
Details 2.6 M ammonium sulfate, 0.1 M sodium phosphate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 29.01 α = 90
b = 46.35 β = 90
c = 57.09 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 2002-02-21
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 15.99 96.9 0.045 -- -- 3.5 42481 41152 -- 2.0 5.84
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)
1.0 1.02 80.7 0.26 -- 3.5 2.9 2042

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 1.0 15.99 -- -- 40686 39319 2096 96.64 -- 0.12221 0.12109 0.14397 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 1.0 1.022 2042 119 2042 0.251 0.272 -- 70.12
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ANISOTROPIC
Mean Isotropic B 10.265
Anisotropic B[1][1] 0.06
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.05
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 6.534
r_sphericity_free 13.637
r_rigid_bond_restr 2.742
r_scangle_it 6.921
r_scbond_it 5.203
r_mcangle_it 3.279
r_mcbond_it 2.528
r_symmetry_hbond_refined 0.385
r_bond_refined_d 0.027
r_angle_refined_deg 2.663
r_dihedral_angle_1_deg 7.443
r_dihedral_angle_2_deg 28.2
r_dihedral_angle_3_deg 10.874
r_chiral_restr 0.164
r_gen_planes_refined 0.013
r_nbd_refined 0.573
r_nbtor_refined 0.329
r_xyhbond_nbd_refined 0.504
r_metal_ion_refined 0.069
r_symmetry_vdw_refined 0.262
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 738
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 213

Software

Computing
Computing Package Purpose
Marccd Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
Molrep Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement
Molrep model building
Marccd data collection