3HML | pdb_00003hml

Crystal Structure of PqqC Active Site Mutant H154S in Complex with PQQ

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OTW	PDB ENTRY 1OTW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	1.0M Ammonium sulfate, 0.1M HEPES pH 7.0, 0.5% w/v Polyethylene glycol 8000, vapor diffusion, sitting drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.06	α = 90
b = 118.291	β = 90
c = 68.04	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR555 FLAT PANEL		2008-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.8148	EMBL/DESY, HAMBURG	X11

Data Collection

Overall
ID #	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	2.35	39.44	99.7	0.107	0.099	13.6	6.7		25868

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.35	2.48	98.4		0.812	0.731	1.7	5.3	3640

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1OTW	2.35	38.37	25842	1311	99.58	0.215	0.212	0.2356	0.261	0.2824	RANDOM	46.347

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.31			-0.03		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.308
r_dihedral_angle_4_deg	17.059
r_dihedral_angle_3_deg	16.905
r_dihedral_angle_1_deg	6.597
r_scangle_it	3.071
r_scbond_it	2.121
r_angle_refined_deg	1.696
r_mcangle_it	1.533
r_mcbond_it	0.949
r_nbtor_refined	0.3
r_nbd_refined	0.21
r_symmetry_vdw_refined	0.209
r_symmetry_hbond_refined	0.166
r_xyhbond_nbd_refined	0.159
r_chiral_restr	0.107
r_bond_refined_d	0.018
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3856
Nucleic Acid Atoms
Solvent Atoms	57
Heterogen Atoms	48

Software

Software
Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction