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_metal_ion_refined 0.069
r_scangle_it 6.921
r_sphericity_bonded 6.534
r_chiral_restr 0.164
r_gen_planes_refined 0.013
r_mcbond_it 2.528
r_dihedral_angle_3_deg 10.874
r_angle_refined_deg 2.663
r_nbd_refined 0.573
r_scbond_it 5.203
r_bond_refined_d 0.027
r_nbtor_refined 0.329
r_sphericity_free 13.637
r_dihedral_angle_1_deg 7.443
r_rigid_bond_restr 2.742
r_dihedral_angle_2_deg 28.2
r_xyhbond_nbd_refined 0.504
r_symmetry_vdw_refined 0.262
r_symmetry_hbond_refined 0.385
r_mcangle_it 3.279
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

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