X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 292.0
Details IsdC at 95mg/ml in 50mM Tris-HCl pH 8.0, 500mM NaCl mixed in equal volumes (2 + 2 l) with reservoir solution containing 26% PEG 550, MME, 18mM zinc sulphate, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.49 α = 90
b = 70.44 β = 90
c = 88.68 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 277
Diffraction Detector
Detector Diffraction Type Details Collection Date
-- -- -- 2006-08-31
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.933, 1.739, 1.741, 1.722 ESRF ID29

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
1.5 47.5 -- 0.03 -- -- 4.3 48228 45711 -- -- --
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)
1.5 1.6 -- 0.43 -- 1.8 4.9 6918

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
MAD 1.5 35.99 -- -- 48228 45711 2433 99.71 -- 0.19487 0.19343 0.22204 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 1.501 1.54 6918 176 3270 0.338 0.4 -- 98.46
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Mean Isotropic B 21.346
Anisotropic B[1][1] 0.19
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.04
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.22
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 2.718
r_sphericity_free 3.95
r_rigid_bond_restr 2.068
r_scangle_it 2.879
r_scbond_it 2.462
r_mcangle_it 1.355
r_mcbond_it 0.954
r_symmetry_metal_ion_refined 0.077
r_symmetry_hbond_refined 0.101
r_symmetry_vdw_refined 0.213
r_bond_refined_d 0.009
r_angle_refined_deg 1.444
r_dihedral_angle_1_deg 6.17
r_dihedral_angle_2_deg 37.366
r_dihedral_angle_3_deg 11.033
r_dihedral_angle_4_deg 6.099
r_chiral_restr 0.078
r_gen_planes_refined 0.005
r_nbd_refined 0.193
r_nbtor_refined 0.301
r_xyhbond_nbd_refined 0.117
r_metal_ion_refined 0.025
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1960
Nucleic Acid Atoms 0
Heterogen Atoms 94
Solvent Atoms 189

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
SHARP Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement