Experiment: 3O3P

Crystal structure of R. xylanophilus MpgS in complex with GDP-Mannose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3F1Y	PDB ENTRY 3F1Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	0.1M MES pH 6.0, 2M NaCl, 0.1M NaH2PO4, 0.1M KH2PO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.37	α = 90
b = 108.37	β = 90
c = 311.96	γ = 120

Symmetry
Space Group	P 65 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	ADSC QUANTUM 315r		2010-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9762	ESRF	ID23-1

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	2.529	69.67	100	0.073	0.073	7.3	6.8		37299			41.62

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)
	2.529	2.67	100		0.526	0.526	0.218	6.7	5300

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	PDB ENTRY 3F1Y	2.529	54.185	0.01	36300	1805	97.47	0.1904	0.1883	0.1686	0.2309	0.2118	random	45.201

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]
4.9722			4.9722		-9.9444

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.973
f_angle_d	1.09
f_chiral_restr	0.073
f_bond_d	0.013
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4959
Nucleic Acid Atoms
Solvent Atoms	130
Heterogen Atoms	71

Software

Software
Software Name	Purpose
MOSFLM	data reduction
PHASES	phasing
PHENIX	refinement
SCALA	data scaling
PHASER	phasing