6ER2 | pdb_00006er2

Ruminococcus gnavus IT-sialidase CBM40

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VW2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M ammonium chloride with 20% PEG 8000 The drop contained 0.5 microlitre protein solution at 25 mg/ml and 0.5 microlitre reservoir solution

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.683	α = 90
b = 72.745	β = 104.94
c = 51.292	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	100	CCD	RIGAKU SATURN 944+		2014-07-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54178

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	1.73	50	91.8	0.034	30.7	3.7		33276

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	1.73	1.76	51.3		0.14		2.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	2vw2	1.73	49.56	31570	1698	91.56	0.1614	0.1596	0.1698	0.194	0.198	RANDOM	19.986

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		-0.92	0.49		-0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.548
r_dihedral_angle_3_deg	12.09
r_dihedral_angle_4_deg	11.415
r_dihedral_angle_1_deg	6.798
r_mcangle_it	2.86
r_mcbond_it	2.074
r_mcbond_other	2.072
r_angle_refined_deg	1.551
r_angle_other_deg	1.255
r_chiral_restr	0.098
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.006
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2788
Nucleic Acid Atoms
Solvent Atoms	338
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data collection
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction