X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9.5
Temperature 293.0
Details MMP-12 at 0.4 mM co-crystallized with 100 mM AHA and compound QEG at 1 mM against reservoir solution: 27% PEG 10000, 100 mM Tris-HCl, pH 9.5. 24h in cryoprotectant to remove AHA. 70 MICRO-M compound QEG in 10% di-ethylene glycol, 10% 1.2-propanediol, 10% glycerol, 10% PEG 10K, 200 mM NaCl, 33.3 mM sodium acetate, 33.3 mM ADA, 33.3 mM bicine, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.71 α = 90
b = 63.06 β = 90
c = 37.95 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD bent cylindrical mirror 2011-02-01
Diffraction Radiation
Monochromator Protocol
horizontally diffracting Si (111) monochromator and Pt coated mirrors in Kirkpatrick-Baez geometry for focusing SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-2 0.87260 ESRF ID23-2

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
2 33.33 83.9 0.142 0.074 -- 3.7 -- 9572 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)
2.0 2.11 80.9 1.066 0.926 1.6 3.4 --

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
RIGID BODY REFINEMENT 2.0 33.331 -- -- 11288 9114 458 80.74 -- 0.1655 0.16216 0.23174 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 2.0 2.052 -- 35 648 0.232 0.339 -- 80.73
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 27.721
Anisotropic B[1][1] -1.44
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.26
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.71
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 2.22
r_mcangle_it 1.756
r_dihedral_angle_4_deg 10.712
r_dihedral_angle_1_deg 6.596
r_dihedral_angle_2_deg 37.632
r_gen_planes_refined 0.01
r_chiral_restr 0.177
r_scangle_it 4.129
r_mcbond_it 1.017
r_dihedral_angle_3_deg 14.952
r_bond_refined_d 0.018
r_scbond_it 2.7
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1246
Nucleic Acid Atoms 0
Heterogen Atoms 45
Solvent Atoms 194

Software

Software
Software Name Purpose
DNA data collection
REFMAC refinement version: 5.5.0109
MOSFLM data reduction
SCALA data scaling
REFMAC phasing version: 5.5.0109