X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4
Temperature 294.0
Details 20% MPD, 0.1 M citric acid, 0.1 M cobalt (II) chloride as an additive, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.88 α = 90
b = 96.06 β = 90
c = 127.07 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 MARRESEARCH BENT MIRROR 2007-08-16
Diffraction Radiation
Monochromator Protocol
TRIANGULAR MONOCHROMATOR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 0.976 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
1.7 20 98.7 -- 0.065 -- 3.3 63138 63138 -- -- 20.7
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)
1.7 1.72 98.0 -- 0.254 3.2 3.1 2460

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
-- 1.7 19.38 -- -- 63135 63135 3230 98.7 0.171 0.171 0.1698 0.1924 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 1.7 1.744 4290 236 4290 0.202 0.222 -- 97.5
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.9
Anisotropic B[1][1] -0.63
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.11
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.74
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.686
r_mcangle_it 1.417
r_nbd_refined 0.222
r_symmetry_vdw_other 0.257
r_mcbond_other 0.0
r_bond_other_d 0.0
r_xyhbond_nbd_refined 0.149
r_nbd_other 0.252
r_nbtor_refined 0.199
r_mcbond_it 0.785
r_symmetry_vdw_refined 0.223
r_angle_refined_deg 1.369
r_chiral_restr 0.079
r_nbtor_other 0.103
r_symmetry_hbond_refined 0.138
r_dihedral_angle_4_deg 18.083
r_gen_planes_refined 0.008
r_dihedral_angle_3_deg 13.786
r_dihedral_angle_2_deg 33.037
r_dihedral_angle_1_deg 5.086
r_bond_refined_d 0.013
r_gen_planes_other 0.01
r_angle_other_deg 3.852
r_scbond_it 2.344
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4319
Nucleic Acid Atoms 445
Heterogen Atoms 13
Solvent Atoms 293

Software

Software
Software Name Purpose
SHELXD phasing
SHELXE model building
DM model building
ARP/wARP model building
REFMAC refinement version: 5.2.0019
MAR345 data collection
DENZO data reduction
SCALEPACK data scaling
DM phasing