3DEE | pdb_00003dee

CRYSTAL STRUCTURE OF A PUTATIVE REGULATORY PROTEIN INVOLVED IN TRANSCRIPTION (NGO1945) FROM NEISSERIA GONORRHOEAE FA 1090 AT 2.25 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.36	277	0.2M magnesium chloride, 8.2% Ethanol, 0.1M Imidazole pH 8.36, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.522	α = 90
b = 31.879	β = 115.8
c = 86.369	γ = 90

Symmetry
Space Group	C 1 2 1

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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2008-05-01	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837,0.97929	SSRL	BL9-2

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	2.1	77.85	87.2	0.088	0.088	5.6	3.1		13583			31.24

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)
1	2.1	2.21	97.9		0.475	0.475	1.5	3.1	2201

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.1	77.85	13555	660	86.47	0.225	0.223	0.23	0.267	0.27	RANDOM	29.623

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]
-1.44		-0.52	3.7		-2.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.706
r_dihedral_angle_4_deg	20.332
r_dihedral_angle_3_deg	11.499
r_dihedral_angle_1_deg	3.139
r_mcangle_it	1.63
r_angle_refined_deg	1.535
r_scangle_it	1.325
r_mcbond_it	1.139
r_angle_other_deg	0.956
r_scbond_it	0.92
r_symmetry_vdw_refined	0.342
r_mcbond_other	0.238
r_symmetry_vdw_other	0.213
r_xyhbond_nbd_refined	0.209
r_symmetry_hbond_refined	0.206
r_nbd_refined	0.202
r_nbd_other	0.185
r_nbtor_refined	0.185
r_chiral_restr	0.095
r_nbtor_other	0.087
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1623
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing