6D5D | pdb_00006d5d

Structure of Caldicellulosiruptor danielii GH48 module of glycoside hydrolase WP_045175321

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4EL8	PDB entry 4EL8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M citric acid, pH 5-6, 20% 2-propanol, 0.05 M trisodium citrate, 14-25% PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.014	α = 90
b = 57.512	β = 103.38
c = 105.957	γ = 90

Symmetry
Space Group	C 1 2 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	Bruker Platinum 135		2016-05-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	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	1.9	50	99.2	0.0613	9.95	5.35		53369

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	96.4		0.3521	1.94	1.99

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	PDB entry 4EL8	1.9	103.08	50559	2577	98.75	0.16598	0.16268	0.17	0.23122	0.24	RANDOM	24.103

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]
0.65		-0.01	0.59		-1.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.673
r_dihedral_angle_4_deg	18.206
r_dihedral_angle_3_deg	15.765
r_dihedral_angle_1_deg	6.941
r_long_range_B_refined	5.34
r_long_range_B_other	5.055
r_scangle_other	3.69
r_mcangle_other	2.726
r_mcangle_it	2.724
r_scbond_it	2.53
r_scbond_other	2.528
r_mcbond_it	2.119
r_mcbond_other	2.087
r_angle_refined_deg	1.726
r_angle_other_deg	1.056
r_chiral_restr	0.118
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5082
Nucleic Acid Atoms
Solvent Atoms	807
Heterogen Atoms	47

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
PROTEUM PLUS	data scaling
MOLREP	phasing