1NZC

The high resolution structures of RmlC from Streptococcus suis in complex with dTDP-D-xylose

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.2	298	0.1 M Tris, 4 mM NiCl2,10 mM dTDP-D-xylose, 35% PEG 2000, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.88	33.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.85	α = 90
b = 140.866	β = 92.72
c = 53.699	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	120	CCD	ADSC QUANTUM 4		2001-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.1	1.488	SRS	PX14.1

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	1.8	50.79	91.8	0.126	0.117	3.8	5.3	63995	63969	2.96	3.1	21.38

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)
	1.8	1.81	43.3		0.112	0.085	8.1	2.1	500

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1NYW	1.8	70.71	2.574	87974	60716	3217	91.8	0.16698	0.16445	0.21562	RANDOM	17.913

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]
-0.44		-0.03	-0.02		0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.41
r_sphericity_free	2.886
r_scangle_it	2.882
r_scbond_it	1.847
r_angle_refined_deg	1.577
r_mcangle_it	1.294
r_rigid_bond_restr	1.119
r_sphericity_bonded	1.069
r_angle_other_deg	0.911
r_mcbond_it	0.747
r_symmetry_hbond_refined	0.35
r_symmetry_vdw_refined	0.289
r_symmetry_vdw_other	0.271
r_nbd_other	0.256
r_nbd_refined	0.196
r_xyhbond_nbd_refined	0.176
r_chiral_restr	0.103
r_nbtor_other	0.089
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_gen_planes_other	0.005
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6304
Nucleic Acid Atoms
Solvent Atoms	874
Heterogen Atoms	138

Software

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