1VMH | pdb_00001vmh

Crystal structure of an uncharacterized conserved protein yjbq/upf0047 family, ortholog yugu b.subtilis (ca_c0907) from clostridium acetobutylicum at 1.31 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VMF	PDB entry 1VMF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	9	277	2.0% Dioxane, 10.0% PEG-20000, 0.1M Bicine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.87	33.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.406	α = 90
b = 79.406	β = 90
c = 50.688	γ = 120

Symmetry
Space Group	H 3

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 315	Flat mirror	2004-07-08	M	SINGLE WAVELENGTH

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

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	1.31	23.13	96.3	0.072	14.6	5.9		27579			22.87

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	1.31	1.38	85.5		0.654	1.7	1.9	3555

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	PDB entry 1VMF	1.31	23.13	26191	1388	96.25	0.15871	0.1574	0.17	0.18503	0.19	RANDOM	15.267

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]
-0.03	-0.01		-0.03		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.518
r_dihedral_angle_4_deg	19.779
r_dihedral_angle_3_deg	12.187
r_dihedral_angle_1_deg	5.497
r_scangle_it	4.714
r_scbond_it	3.291
r_mcangle_it	2.361
r_mcbond_it	1.483
r_angle_refined_deg	1.339
r_angle_other_deg	0.785
r_mcbond_other	0.452
r_symmetry_vdw_refined	0.36
r_nbd_refined	0.208
r_symmetry_hbond_refined	0.194
r_nbtor_refined	0.176
r_nbd_other	0.171
r_symmetry_vdw_other	0.167
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.097
r_nbtor_other	0.083
r_symmetry_metal_ion_refined	0.066
r_metal_ion_refined	0.062
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	995
Nucleic Acid Atoms
Solvent Atoms	159
Heterogen Atoms	1

Software

Software
Software Name	Purpose
XDS	data scaling
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
CCP4	data scaling