X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 293.0
Details MMP-8 at 400 micro-M co-crystallization with peptidic inhibitor with reservoir solution 17.5% PEG 20K, 0.1 M MES, 0.125 M NACL. VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K. Inhibitor exchange: 24hr soak in 25% PEG 4K instead of 17.5% PEG20K with 100 micro-M E1S inhibitor in 6 micro-L volume cryoprotectant is 12% PEG10K, 13.75% MPEG2K, 5% di-ethylene glycol, 10% 1,2-propanediol, 10% glycerol, 0.025 M MES PH 5.5, 30 sec cryoprotectant soak

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 32.72 α = 90
b = 69.37 β = 90
c = 70.31 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 ADSC QUANTUM 315r bent cylindrical mirror 2011-06-13
Diffraction Radiation
Monochromator Protocol
horizontally diffracting Si (111) monochromator and Pt coated mirrors in Kirkpatrick-Baez geometry for focussing SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.97242 ESRF ID23-1

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
1.88 60 98.1 0.247 0.222 -- 5.26 13650 13397 0.0 -3.0 24.39
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)
1.88 2.01 99.6 1.026 0.919 2.08 5.2 12439

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 1.88 34.69 -- 0.0 12970 12729 667 98.14 -- 0.19409 0.19087 0.2578 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 1.88 1.929 -- 58 945 0.325 0.424 -- 99.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 21.835
Anisotropic B[1][1] -1.73
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.79
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.53
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 1.278
r_angle_refined_deg 2.012
r_dihedral_angle_4_deg 21.05
r_mcangle_it 2.071
r_scbond_it 3.103
r_scangle_it 4.249
r_dihedral_angle_1_deg 7.547
r_dihedral_angle_2_deg 33.691
r_bond_refined_d 0.022
r_chiral_restr 0.24
r_dihedral_angle_3_deg 16.025
r_gen_planes_refined 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1253
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 171

Software

Software
Software Name Purpose
DNA data collection
MOLREP phasing
REFMAC refinement version: 5.5.0109
XDS data reduction
XSCALE data scaling