Experiment: 21EJ

Crystal structure of a cupin protein (tm1459, H52A mutant) soaked in CuSO4

X-RAY DIFFRACTION

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
2.06	40.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.736	α = 90
b = 57.794	β = 90
c = 75.21	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		2025-06-19	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	1.035	34.01	99.1	0.022	0.999	22.74	3.38		206099

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	1.035	1.1	98.1		0.563	0.767	2.07	3.28

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	1.035	34.01	195792	10307	99.1	0.1413	0.1413	0.1404	0.1329	0.1764	0.1604	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	0.5257
s_from_restr_planes	0.4195
s_approx_iso_adps	0.17
s_zero_chiral_vol	0.1006
s_similar_adp_cmpnt	0.0571
s_rigid_bond_adp_cmpnt	0.035
s_angle_d	0.0247
s_bond_d	0.0131
s_similar_dist
s_anti_bump_dis_restr

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1862
Nucleic Acid Atoms
Solvent Atoms	275
Heterogen Atoms	31

Software

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.