X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8
Temperature 293.0
Details Protein: MMP9h Nter=GFQT E402Q V391Q at 130.3 micro-M with 5 milli-M AHA Reservoir: 40% MPEG 5K, 100mM HEPES. Cryoprotectant: 35% MPEG 5K, 15% PEG 400, 15% AAB (90/10), pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 44.14 α = 90
b = 48.66 β = 102.55
c = 67.92 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4r MIRRORS 2010-11-24
Diffraction Radiation
Monochromator Protocol
DIAMOND (111), GE(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 -- ESRF ID14-1

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
1.59 50 96.8 0.0124 0.109 -- 4.3 -- 36921 -- -3.0 21.71
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)
1.59 1.68 94.7 1.229 1.076 1.35 4.06 --

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 1.59 43.09 -- 1.99 36921 36919 1846 96.8 -- 0.172 0.17 0.211 --
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 1.5886 1.6315 -- 137 2606 0.2741 0.3163 -- 94.0
X Ray Diffraction 1.6315 1.6796 -- 139 2654 0.2549 0.3236 -- 96.0
X Ray Diffraction 1.6796 1.7338 -- 140 2662 0.2305 0.2677 -- 96.0
X Ray Diffraction 1.7338 1.7957 -- 139 2625 0.2076 0.2621 -- 96.0
X Ray Diffraction 1.7957 1.8676 -- 141 2685 0.1945 0.2309 -- 96.0
X Ray Diffraction 1.8676 1.9526 -- 139 2647 0.1734 0.2451 -- 96.0
X Ray Diffraction 1.9526 2.0556 -- 143 2719 0.1592 0.1876 -- 97.0
X Ray Diffraction 2.0556 2.1844 -- 142 2687 0.1539 0.2037 -- 97.0
X Ray Diffraction 2.1844 2.353 -- 143 2724 0.1583 0.198 -- 98.0
X Ray Diffraction 2.353 2.5898 -- 143 2717 0.1602 0.207 -- 98.0
X Ray Diffraction 2.5898 2.9644 -- 145 2742 0.1584 0.2148 -- 98.0
X Ray Diffraction 2.9644 3.7346 -- 145 2761 0.1456 0.1718 -- 99.0
X Ray Diffraction 3.7346 43.1012 -- 150 2844 0.1574 0.1838 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 21.7
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_chiral_restr 0.083
f_dihedral_angle_d 24.462
f_angle_d 1.472
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2550
Nucleic Acid Atoms 0
Heterogen Atoms 167
Solvent Atoms 326

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
MOLREP Structure Solution
PHENIX (PHENIX.REFINE: 1.8_1069) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8_1069) refinement
MOLREP model building
DNA data collection