7NWP | pdb_00007nwp

A carbohydrate binding module family 9 (CBM9) from Caldicellulosiruptor kristjansonii in complex with cellobiose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1I8U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	293	0.1 M phosphate-citrate and 40% polyethylene glycol 300

Crystal Properties
Matthews coefficient	Solvent content
4.4	72.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 173.32	α = 90
b = 173.32	β = 90
c = 173.32	γ = 90

Symmetry
Space Group	I 4 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2019-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.000000	PETRA III, DESY	P11

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	2.163	46.365	99.95	1	34.46	78.5		23991

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	2.163	2.24			0.542

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1i8u	2.163	46.365	23989	2400	99.954	0.183	0.179	0.18	0.219	0.22	52.546

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.946
r_dihedral_angle_4_deg	22.231
r_dihedral_angle_3_deg	16.31
r_lrange_it	9.836
r_dihedral_angle_1_deg	8.442
r_scangle_it	7.995
r_mcangle_it	7.097
r_scbond_it	6.023
r_mcbond_it	5.179
r_angle_refined_deg	1.715
r_nbtor_refined	0.316
r_nbd_refined	0.215
r_metal_ion_refined	0.168
r_symmetry_nbd_refined	0.157
r_symmetry_xyhbond_nbd_refined	0.145
r_xyhbond_nbd_refined	0.123
r_chiral_restr	0.117
r_bond_refined_d	0.01
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1575
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	phasing