X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 295.0
Details 7,5% Na malonate, 20mM AcNa, 100 mM glycine, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.47 α = 90
b = 57.55 β = 90
c = 101.39 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 MARMOSAIC 225 mm CCD mirrors 2005-10-28
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 -- EMBL/DESY, Hamburg X12

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
1.9 20.64 90.7 0.161 0.072 -- 2.47 -- 21425 0.0 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)
1.9 2.01 83.8 0.511 0.327 2.34 2.38 3129

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 1.9 20.64 -- 0.0 -- 21425 1146 97.64 0.21524 0.21524 0.2127 0.26411 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 1.9 1.949 1511 80 1511 0.251 0.304 -- 93.98
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.629
Anisotropic B[1][1] -0.07
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.21
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.14
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.163
r_symmetry_vdw_refined 0.185
r_dihedral_angle_1_deg 5.681
r_nbd_refined 0.211
r_rigid_bond_restr 2.492
r_gen_planes_refined 0.006
r_dihedral_angle_2_deg 43.382
r_dihedral_angle_3_deg 18.855
r_mcbond_it 1.799
r_dihedral_angle_4_deg 15.084
r_angle_refined_deg 1.535
r_chiral_restr 0.11
r_sphericity_bonded 15.262
r_scbond_it 3.452
r_sphericity_free 9.796
r_scangle_it 4.927
r_bond_refined_d 0.015
r_symmetry_hbond_refined 0.129
r_mcangle_it 2.806
r_nbtor_refined 0.312
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2144
Nucleic Acid Atoms 0
Heterogen Atoms 9
Solvent Atoms 134

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
XDS data reduction
XDS data scaling
PHASER phasing version: 1.3.2b1