5L2V | pdb_00005l2v

Catalytic domain of LPMO Lmo2467 from Listeria monocytogenes

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		297	Protein: 8.0 mg/ml, 0.01 M Tris HCl (pH 8.3); Screen: JCSG+ H9 (Qiagen),0.2 M AmSO4, 0.1 M Bis-Tris (pH 5.5), 25% (w/v) PEG3350.

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.575	α = 90
b = 139.712	β = 90
c = 90.591	γ = 90

Symmetry
Space Group	C 2 2 21

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 300 mm CCD		2016-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	.978	APS	21-ID-G

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	1.1	30	94.8	0.079	21.6	6.7		148923

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	1.1	1.12	66.9		0.749	1.6	3.9

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	2BEM	1.1	29.15	141504	7382	95.5	0.129	0.129	0.13	0.145	0.15	RANDOM	13.23

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]
-0.3			-0.15		0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.238
r_sphericity_free	27.415
r_dihedral_angle_4_deg	11.085
r_dihedral_angle_3_deg	9.951
r_dihedral_angle_1_deg	6.609
r_sphericity_bonded	6.34
r_long_range_B_refined	3.149
r_long_range_B_other	1.766
r_angle_refined_deg	1.428
r_rigid_bond_restr	0.939
r_angle_other_deg	0.926
r_scangle_other	0.877
r_scbond_it	0.751
r_scbond_other	0.748
r_mcangle_it	0.699
r_mcangle_other	0.699
r_mcbond_it	0.525
r_mcbond_other	0.523
r_chiral_restr	0.086
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2534
Nucleic Acid Atoms
Solvent Atoms	620
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing