3BQF

Structure of the central domain (MsrA) of Neisseria meningitidis PilB (complex with a substrate)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BQE	PDB ENTRY 3BQE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	microbatch-under-oil	9	293	1 volume of 30% PEG 550 MME, 0.1M Bicine pH 9.0, 0.1M NaCl, mixed with 1 volume of 50mM TRIS HCl, 2mM EDTA pH 8, 18mg/mL protein + 200mM AcMet(R,S)SONHMe, microbatch-under-oil, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.679566	26.766775

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.933	α = 90
b = 50.305	β = 90
c = 66.556	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MAR CCD 165 mm	Bent Mirror	2003-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.81	EMBL/DESY, HAMBURG	X11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.22	20	97.5	0.078	15.3	4.1	7685	7491			15.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.24	2.28	99.7		0.265	4.24	4.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (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 3BQE	2.24	19.8	7475	7169	694	95.9	0.185	0.18	0.209	0.21	RANDOM	25.6

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]
1.08			-0.93		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.3
c_scangle_it	2.36
c_mcangle_it	2.08
c_scbond_it	1.59
c_mcbond_it	1.33
c_angle_deg	1.2
c_improper_angle_d	0.67
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1341
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms	14

Software

Software
Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.