2OPD | pdb_00002opd

Structure of the Neisseria meningitidis minor Type IV pilin, PilX

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		P43 space group PilX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	Protein at 7 mg/ml in 25 mM KCl, 50 mM Hepes, pH 7.5 was mixed in a 1:1 ratio with unbuffered 4 M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.128	α = 90
b = 83.366	β = 90
c = 105.323	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	98	CCD	BRUKER PROTEUM	Montel 200	2005-06-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.5	30	99.8	0.074	17.5	8.6		10281			58.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.5	2.59	100		0.277	6.3	7.1	999

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	P43 space group PilX	2.5	25	9740	510	99.17	0.205	0.204	0.2436	0.236	0.2674	RANDOM	52.283

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]
0.66			-0.02		-0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.329
r_dihedral_angle_4_deg	16.993
r_dihedral_angle_3_deg	16.529
r_dihedral_angle_1_deg	6.813
r_scangle_it	2.642
r_scbond_it	1.858
r_angle_refined_deg	1.639
r_mcangle_it	1.097
r_mcbond_it	0.664
r_symmetry_hbond_refined	0.329
r_nbtor_refined	0.325
r_nbd_refined	0.245
r_symmetry_vdw_refined	0.237
r_xyhbond_nbd_refined	0.207
r_chiral_restr	0.117
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1908
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing