2P5V | pdb_00002p5v

Crystal Structure of Transcriptional Regulator NMB0573 from Neisseria Meningitidis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	95 mM HEPES-Na, 190 mM Calcium Chloride, 26.6% PEG 400, 5% Glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.07	α = 90
b = 148.48	β = 106.41
c = 77.72	γ = 90

Symmetry
Space Group	P 1 21 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 225 mm CCD	mirrors	2005-05-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.9795, 0.9078	ESRF	BM14

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	30	77.7	0.082	20.2	7.4		74733		-1.5	26

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	2.07	29.9		0.424	2.4	3.4	2860

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	1.99	29.59	70865	3804	77.14	0.17933	0.17624	0.1867	0.23785	0.2422	RANDOM	39.879

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]
2.85		4	-0.58		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.527
r_dihedral_angle_4_deg	14.081
r_dihedral_angle_3_deg	14.076
r_scangle_it	8.789
r_scbond_it	6.354
r_dihedral_angle_1_deg	5.566
r_mcangle_it	4.711
r_mcbond_it	3.667
r_mcbond_other	1.27
r_angle_refined_deg	1.1
r_angle_other_deg	0.821
r_symmetry_vdw_other	0.235
r_symmetry_vdw_refined	0.201
r_nbd_refined	0.195
r_nbd_other	0.188
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.161
r_symmetry_hbond_refined	0.113
r_metal_ion_refined	0.097
r_nbtor_other	0.085
r_chiral_restr	0.059
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9844
Nucleic Acid Atoms
Solvent Atoms	760
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing