7QLJ | pdb_00007qlj

Trans structure of rsKiiro Illuminated at 290 K

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5OOZ
experimental model	PDB	5OQA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	8.4	295	0.2 M lithium sulfate, 0.1 M Tris-Cl, 25 % PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.747	α = 90
b = 73.524	β = 90
c = 78.106	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	100	PIXEL	DECTRIS PILATUS 6M-F		2018-01-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.02	39.053	98.9	0.061	0.999	12.8	6.1		112855

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.02	1.039			0.777	0.593	2.2

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	5OOZ, 5OQA	1.02	39.053	112852	5501	98.892	0.119	0.1186	0.12	0.1367	0.14	11.113

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]
0.029			-0.16		0.132

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.321
r_dihedral_angle_4_deg	18.577
r_dihedral_angle_3_deg	11.752
r_dihedral_angle_1_deg	6.979
r_rigid_bond_restr	4.675
r_lrange_it	3.523
r_lrange_other	3.26
r_scangle_it	2.935
r_scangle_other	2.92
r_scbond_it	2.669
r_scbond_other	2.664
r_angle_refined_deg	2.546
r_mcangle_it	2.249
r_mcangle_other	2.249
r_mcbond_it	1.91
r_mcbond_other	1.905
r_angle_other_deg	1.542
r_symmetry_nbd_refined	0.582
r_symmetry_xyhbond_nbd_refined	0.235
r_xyhbond_nbd_refined	0.206
r_nbd_refined	0.203
r_symmetry_nbd_other	0.192
r_nbd_other	0.188
r_nbtor_refined	0.181
r_chiral_restr	0.12
r_symmetry_nbtor_other	0.096
r_bond_refined_d	0.021
r_symmetry_xyhbond_nbd_other	0.017
r_gen_planes_refined	0.012
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1770
Nucleic Acid Atoms
Solvent Atoms	260
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
REFMAC	phasing