3GDB

Crystal structure of Spr0440 glycoside hydrolase domain, Endo-D from Streptococcus pneumoniae R6

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	289	20% w/v Polyethylene glycol 4000, 0.1M Sodium acetate trihydrate pH 4.6, 10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
1.704281	27.828815

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.14	α = 90
b = 59.06	β = 110.27
c = 94.89	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	IMAGE PLATE	MAR scanner 345 mm plate		2008-12-06	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MAR CCD 165 mm		2008-01-18	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418
2	SYNCHROTRON	BSRF BEAMLINE 3W1A	0.9790,0.9793,0.9700	BSRF	3W1A

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	1.86	24.66	97.1	0.066	0.078	14.7	3.4		57291			20.9

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)
	1.86	1.98	88.4		0.406	0.482	3.1	3.3	7581

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.87	24.66	54391	2899	97.74	0.16352	0.16128	0.20435	RANDOM	21.169

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]
-1.76		-1.16	-0.94		1.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.744
r_dihedral_angle_4_deg	18.1
r_dihedral_angle_3_deg	14.761
r_dihedral_angle_1_deg	6.67
r_scangle_it	3.433
r_scbond_it	2.399
r_angle_refined_deg	1.389
r_mcangle_it	1.273
r_mcbond_it	0.95
r_nbtor_refined	0.305
r_symmetry_vdw_refined	0.218
r_nbd_refined	0.19
r_symmetry_hbond_refined	0.149
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.106
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5068
Nucleic Acid Atoms
Solvent Atoms	727
Heterogen Atoms	10

Software

Software
Software Name	Purpose
MAR345dtb	data collection
SOLVE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALEPACK	data scaling