7LSA | pdb_00007lsa

Ruminococcus bromii Amy12 with maltoheptaose

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	well solution: 16% PEG 3350, 4% glycerol, 0.3 ammonium acetate, and 0.1 M Bis-Tris pH 6.5; protein: 8.75 - 8.9 mg/ml Amy12 with 10mM maltoheptaose

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.977	α = 90
b = 97.96	β = 90
c = 167.089	γ = 90

Symmetry
Space Group	P 21 21 21

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	RAYONIX MX300-HS		2015-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.979	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.76	48.46	95.9	0.99	8.6	4.7		74259

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.76	1.82			0.26

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	2WAN	1.76	48.46	72050	2010	95.57	0.1604	0.1592	0.1706	0.2064	0.218	RANDOM	19.913

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]
-0.55			0.2		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.897
r_sphericity_free	20.287
r_dihedral_angle_4_deg	15.86
r_dihedral_angle_3_deg	11.306
r_sphericity_bonded	7.256
r_dihedral_angle_1_deg	6.845
r_angle_refined_deg	0.992
r_angle_other_deg	0.823
r_rigid_bond_restr	0.464
r_chiral_restr	0.049
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5871
Nucleic Acid Atoms
Solvent Atoms	720
Heterogen Atoms	146

Software

Software
Software Name	Purpose
xia2	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction