6YP1 | pdb_00006yp1

HiCel7B unliganded

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2A39

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	298	12 mg/mL protein in 20 mM pH 8 Tris-HCl mixed 2:1 with 0.15 M sodium citrate, 0.8 M ammonium sulfate, 1 M lithium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.31	α = 90
b = 92.31	β = 90
c = 100.81	γ = 90

Symmetry
Space Group	P 42 21 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 EIGER2 X 16M		2019-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.2	46.198	99.8	0.053	26.7	14		135228

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.22	96.3		0.483	3.2

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	2A39	1.2	46.198	135228	6795	99.683	0.118	0.1167	0.12	0.1353	0.14	12.949

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]
0.352			0.352		-0.704

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.367
r_dihedral_angle_4_deg	15.444
r_dihedral_angle_3_deg	11.715
r_rigid_bond_restr	8.186
r_dihedral_angle_1_deg	6.763
r_scbond_other	4.99
r_scbond_it	4.989
r_scangle_it	4.605
r_scangle_other	4.604
r_lrange_it	3.818
r_lrange_other	3.632
r_angle_refined_deg	2.32
r_angle_other_deg	1.718
r_mcangle_it	1.485
r_mcangle_other	1.485
r_mcbond_it	1.18
r_mcbond_other	1.18
r_symmetry_nbd_refined	0.326
r_symmetry_xyhbond_nbd_refined	0.263
r_nbd_refined	0.257
r_nbd_other	0.23
r_symmetry_nbd_other	0.211
r_xyhbond_nbd_refined	0.206
r_nbtor_refined	0.181
r_symmetry_xyhbond_nbd_other	0.136
r_chiral_restr	0.131
r_symmetry_nbtor_other	0.098
r_bond_refined_d	0.024
r_gen_planes_refined	0.013
r_bond_other_d	0.006
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3073
Nucleic Acid Atoms
Solvent Atoms	391
Heterogen Atoms	115

Software

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