9XS8 | pdb_00009xs8

Crystal structure of a cupin protein (tm1459, H52A/H54A/H92A/C106E mutant) in ruthenium(p-cymene) bound form

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	25% w/v Jeffamine ED-2001, 0.1M MES

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.81	α = 90
b = 57.63	β = 90
c = 74.5	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 EIGER X 16M		2023-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.899995	SPring-8	BL44XU

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	1.265	50	99.4	0.044	0.998	13.79	3.4		112232

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	1.265	1.34	98.9		0.581	0.723	2.03	3.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	FREE R-VALUE	1.265	50	112232	5607	99.4	0.1487	0.1487	0.1474	0.1426	0.1981	0.1938	RANDOM

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
s_non_zero_chiral_vol	0.6706
s_from_restr_planes	0.433
s_approx_iso_adps	0.1665
s_zero_chiral_vol	0.098
s_similar_adp_cmpnt	0.0652
s_rigid_bond_adp_cmpnt	0.0401
s_angle_d	0.0257
s_bond_d	0.0098
s_similar_dist
s_anti_bump_dis_restr

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3641
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms

Software

Software
Software Name	Purpose
SHELXL	refinement
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling