2NT4 | pdb_00002nt4

Receiver domain from Myxococcus xanthus social motility protein FrzS (H92F mutant)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GKG	pdb entry 2gkg

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291	100mM Bis-Tris pH 5.5, 25% PEG 3350, 20% MPD added before freezing, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.883	α = 90
b = 37.119	β = 102.49
c = 42.104	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	ADSC QUANTUM 210		2006-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1		ALS	8.3.1

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	1.02	20	96.7	0.043	0.043	14.3	3.5	51807	51807			6.5

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)
	1.02	1.08	82.4		0.327	0.327	2	2.2	6553

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-Factor (All)	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	pdb entry 2gkg	1.02	20	51778	51778	2625	96.62	0.1241	0.1241	0.12253	0.13	0.1539	0.16	RANDOM	8.627

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]
0.07		-0.37	-0.05		-0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.996
r_dihedral_angle_4_deg	14.626
r_dihedral_angle_3_deg	10.535
r_dihedral_angle_1_deg	6.489
r_sphericity_free	5.938
r_scangle_it	4.325
r_scbond_it	3.156
r_sphericity_bonded	2.697
r_mcangle_it	2.017
r_mcbond_it	1.654
r_angle_refined_deg	1.539
r_rigid_bond_restr	1.457
r_angle_other_deg	0.849
r_mcbond_other	0.524
r_symmetry_vdw_other	0.311
r_nbd_refined	0.239
r_symmetry_vdw_refined	0.225
r_symmetry_hbond_refined	0.218
r_nbd_other	0.186
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.156
r_symmetry_hbond_other	0.152
r_chiral_restr	0.096
r_nbtor_other	0.082
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.004
r_gen_planes_other	0.003
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	958
Nucleic Acid Atoms
Solvent Atoms	246
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing