3M8D | pdb_00003m8d

Crystal structure of spin-labeled BtuB V10R1 with bound calcium and cyanocobalamin

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.6	290	2.5% PEG3350, 150 mM calcium chloride, 20 mM Bis tris, 10 mM C8E4, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
3.28	62.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.051	α = 90
b = 82.051	β = 90
c = 224.457	γ = 120

Symmetry
Space Group	P 31 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	90	CCD	MARMOSAIC 300 mm CCD		2009-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.00	APS	22-ID

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	2.44	50	96.7	0.121	11.1	9.1	32358	32358	4.9	2

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	2.44	2.54	72.4		0.458		3.5	2370

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.44	44.04	30642	32289	1647	96.57	0.279	0.229	0.226	0.23	0.275	0.28	RANDOM	37.685

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]
-0.01			-0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.674
r_dihedral_angle_4_deg	21.72
r_dihedral_angle_3_deg	14.35
r_dihedral_angle_1_deg	9.025
r_scangle_it	4.014
r_scbond_it	2.514
r_angle_refined_deg	2.037
r_mcangle_it	1.645
r_angle_other_deg	0.969
r_mcbond_it	0.899

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.674
r_dihedral_angle_4_deg	21.72
r_dihedral_angle_3_deg	14.35
r_dihedral_angle_1_deg	9.025
r_scangle_it	4.014
r_scbond_it	2.514
r_angle_refined_deg	2.037
r_mcangle_it	1.645
r_angle_other_deg	0.969
r_mcbond_it	0.899
r_mcbond_other	0.186
r_chiral_restr	0.107
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4552
Nucleic Acid Atoms
Solvent Atoms	76
Heterogen Atoms	234

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.