3IMM | pdb_00003imm

Crystal structure of Putative glycosyl hydrolase (YP_001301887.1) from Parabacteroides distasonis ATCC 8503 at 2.00 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	0.2000M NaCl, 30.0000% PEG-3000, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.404	α = 90
b = 45.404	β = 90
c = 241.069	γ = 120

Symmetry
Space Group	P 31

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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2009-04-15	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91162,0.97805,0.97874	SSRL	BL11-1

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	28.105	99.7	0.078	0.078	9.7	2.9		37531			26.958

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	2	2.05	96.9		0.368	0.368	2.2	2.5	2709

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2	28.105	37453	1876	99.73	0.166	0.163	0.17	0.222	0.23	RANDOM	31.58

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]
1.59	0.79		1.59		-2.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.094
r_dihedral_angle_4_deg	17.677
r_dihedral_angle_3_deg	14.292
r_dihedral_angle_1_deg	7.051
r_scangle_it	3.681
r_scbond_it	2.769
r_mcangle_it	2.204
r_angle_refined_deg	1.529
r_mcbond_it	1.492
r_angle_other_deg	0.918
r_mcbond_other	0.688
r_symmetry_vdw_other	0.277
r_nbd_refined	0.214
r_nbd_other	0.193
r_symmetry_vdw_refined	0.189
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.154
r_symmetry_hbond_refined	0.133
r_metal_ion_refined	0.117
r_chiral_restr	0.098
r_nbtor_other	0.088
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4669
Nucleic Acid Atoms
Solvent Atoms	395
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction