3BFM | pdb_00003bfm

Crystal structure of a biotin protein ligase-like protein of unknown function (tm1040_0394) from silicibacter sp. tm1040 at 1.70 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	NANODROP, 0.2M Ca(OAc)2, 40.0% PEG 400, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.76	α = 90
b = 36.56	β = 99.28
c = 71	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 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2007-10-26	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.91840, 0.97953, 0.97939	APS	23-ID-D

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	1.7	29.553	97.5	0.076	7.08	3.33		24223		-3	21.03

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	1.7	1.8	95.1		0.532	1.6

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	1.7	29.553	24219	1211	98.78	0.182	0.179	0.18	0.226	0.23	RANDOM	20.605

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		0.71	-0.44		0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.898
r_dihedral_angle_4_deg	15.23
r_dihedral_angle_3_deg	13.139
r_scangle_it	7.548
r_dihedral_angle_1_deg	5.641
r_scbond_it	5.148
r_mcangle_it	3.237
r_mcbond_it	2.14
r_angle_refined_deg	1.458
r_angle_other_deg	0.931
r_mcbond_other	0.56
r_symmetry_vdw_other	0.237
r_symmetry_hbond_refined	0.217
r_nbd_refined	0.216
r_nbd_other	0.203
r_symmetry_vdw_refined	0.19
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.153
r_nbtor_other	0.088
r_chiral_restr	0.077
r_metal_ion_refined	0.055
r_bond_refined_d	0.015
r_symmetry_metal_ion_refined	0.006
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	1704
Nucleic Acid Atoms
Solvent Atoms	169
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
SHARP	phasing