X-RAY DIFFRACTION Experimental Data & Validation

X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 293.0
Details Protein: hMMP12 F171D at4 784 mico-M + 10 milli-M AHA Reservoir: 12% PEG 20K, 0.14 M imidazole malate, .0175 M NaCl Cryoprotectant: 40% C7 (C7 = 12.5 % di-ethylene glycol + 12.5 % ethylene glycol + 25 % 1,2-propanediol + 12.5 % DMSO + 12.5 % glycerol), 1M NaCl, 0.1 M (MMT buffer 75% acid/25% basic), 9% PEG 10.000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.14 α = 90
b = 62.79 β = 90
c = 113.14 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 MIRRORS 2012-06-14
Diffraction Radiation
Monochromator Protocol
Single Silicon (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.9763 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
1.59 50 98.6 0.159 0.147 -- 7.68 41050 40489 0.0 -3.0 21.449
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 1.69 92.6 0.957 0.892 3.13 7.47 6540

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 1.592 42.029 -3.0 2.02 40489 40486 2024 98.64 -- 0.1729 0.1711 0.2062 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 1.5924 1.6323 2270 120 2270 0.2899 0.3273 -- 83.0
X Ray Diffraction 1.6323 1.6764 2774 146 2774 0.2288 0.2873 -- 100.0
X Ray Diffraction 1.6764 1.7257 2727 143 2727 0.2056 0.2576 -- 100.0
X Ray Diffraction 1.7257 1.7814 2742 144 2742 0.1915 0.2474 -- 100.0
X Ray Diffraction 1.7814 1.8451 2770 146 2770 0.1808 0.2029 -- 100.0
X Ray Diffraction 1.8451 1.919 2748 145 2748 0.176 0.2114 -- 100.0
X Ray Diffraction 1.919 2.0063 2752 145 2752 0.1726 0.1938 -- 100.0
X Ray Diffraction 2.0063 2.1121 2774 146 2774 0.1648 0.234 -- 100.0
X Ray Diffraction 2.1121 2.2444 2756 145 2756 0.1672 0.2075 -- 100.0
X Ray Diffraction 2.2444 2.4177 2779 146 2779 0.1671 0.2229 -- 100.0
X Ray Diffraction 2.4177 2.6609 2797 147 2797 0.1627 0.1844 -- 100.0
X Ray Diffraction 2.6609 3.0459 2802 148 2802 0.1618 0.2028 -- 100.0
X Ray Diffraction 3.0459 3.8371 2859 150 2859 0.1484 0.1817 -- 100.0
X Ray Diffraction 3.8371 42.0431 2912 153 2912 0.1612 0.1748 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 21.4
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.167
f_dihedral_angle_d 16.957
f_angle_d 1.262
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2492
Nucleic Acid Atoms 0
Heterogen Atoms 181
Solvent Atoms 273

Software

Computing
Computing Package Purpose
DNA Data Collection
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