9GUH | pdb_00009guh

Crystal structure of NtcA from S. elongatus in apo form B

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XKP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294.15	NtcA protein was at 6,1 mg/ml in 50 mM sodium citrate pH 6.5, 0.5 M NaCl, 5 mM magnesium cloride, 50 mM arginine hydrocloride, 50 mM Na L-glutamate. CRYSTALLIZATION SOLUTION: 0,05 M Tris-HCL pH8, 2M NaCl, 2% 2-methyl-2,4-pentanediol,10mM MgCl2, 5%DMSO. CRYO PROTECTANT: 27% 2-methyl-2,4-pentanediol

Crystal Properties
Matthews coefficient	Solvent content
3.42	64.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.385	α = 90
b = 96.385	β = 90
c = 126.893	γ = 120

Symmetry
Space Group	P 64 2 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	CCD	MARMOSAIC 225 mm CCD		2010-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.9762	ESRF	BM14

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	3.3	83.5	100	0.136	4	6.6		5530

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)
1	3.3	3.51			0.419

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	MOLECULAR REPLACEMENT	THROUGHOUT	3.33	48.19	5253	247	99.91	0.22441	0.22198	0.2272	0.27392	0.2736	RANDOM	61.692

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]
-0.29	-0.15		-0.29		0.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	19.655
r_long_range_B_refined	11.654
r_long_range_B_other	11.649
r_dihedral_angle_2_deg	10.78
r_scangle_other	8.454
r_mcangle_other	7.879
r_mcangle_it	7.868
r_dihedral_angle_1_deg	6.321
r_scbond_it	5.659
r_scbond_other	5.656
r_mcbond_it	5.125
r_mcbond_other	5.085
r_angle_refined_deg	1.52
r_angle_other_deg	0.506
r_chiral_restr	0.063
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1657
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
XDS	data reduction
MOLREP	phasing