X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 293.0
Details Protein: 6 microL hMMP9(E402A) at 181 micro-M 0.12 M acetohydroxamic acid and 0.3 microL IT34-I at 6.9 mill-M. Reservoir: 10% PEG 20K, 0.1 M MMT (L-malic acid, MES, Tris) 75% acid/25% basic, 0.8 M NaCl, 0.02 SrCl2, 0.01% azide. Cryoprotectant: CryoProtX CM2, 0.8 M Li formate, 0.1 M (MMT 75% acid/25% basic), 9% PEG 10K, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 34.2 α = 90
b = 57.4 β = 90
c = 172.03 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
PIXEL DECTRIS PILATUS 6M mirrors 2012-02-17
Diffraction Radiation
Monochromator Protocol
Channel cut Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9184 SOLEIL PROXIMA 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
1.7 50 99.7 0.174 0.168 -- 8.97 38532 38427 0.0 -3.0 23.385
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 1.8 98.5 1.052 1.083 2.06 8.92 6144

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 1.698 40.568 -3.0 2.01 38427 38419 1922 99.75 0.1602 0.1615 0.1597 0.1954 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 1.6977 1.7402 2604 130 2474 0.2362 0.2793 -- 97.0
X Ray Diffraction 1.7402 1.7872 2722 137 2585 0.2031 0.238 -- 100.0
X Ray Diffraction 1.7872 1.8398 2678 133 2545 0.1877 0.2247 -- 100.0
X Ray Diffraction 1.8398 1.8992 2752 138 2614 0.1719 0.2039 -- 100.0
X Ray Diffraction 1.8992 1.9671 2678 134 2544 0.1579 0.1966 -- 100.0
X Ray Diffraction 1.9671 2.0458 2711 136 2575 0.1564 0.2036 -- 100.0
X Ray Diffraction 2.0458 2.1389 2766 138 2628 0.1436 0.1806 -- 100.0
X Ray Diffraction 2.1389 2.2517 2696 135 2561 0.1478 0.1606 -- 100.0
X Ray Diffraction 2.2517 2.3927 2746 137 2609 0.1518 0.1881 -- 100.0
X Ray Diffraction 2.3927 2.5775 2723 136 2587 0.1567 0.1886 -- 100.0
X Ray Diffraction 2.5775 2.8368 2774 139 2635 0.162 0.225 -- 100.0
X Ray Diffraction 2.8368 3.2471 2775 139 2636 0.1641 0.2347 -- 100.0
X Ray Diffraction 3.2471 4.0904 2820 141 2679 0.1385 0.1648 -- 100.0
X Ray Diffraction 4.0904 40.5794 2974 149 2825 0.1618 0.1802 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 18.68
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.084
f_dihedral_angle_d 16.904
f_chiral_restr 0.08
f_bond_d 0.006
f_plane_restr 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2764
Nucleic Acid Atoms 0
Heterogen Atoms 61
Solvent Atoms 410

Software

Software
Software Name Purpose
DNA data collection
MOLREP phasing
PHENIX refinement version: (phenix.refine: 1.8_1069)
XDS data reduction
XDS data scaling