Experiment: 6L2E

Crystal structure of a cupin protein (tm1459, H52A mutant) in copper (Cu) substituted form

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
2.05	39.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.625	α = 90
b = 57.763	β = 90
c = 75.035	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	CCD	RAYONIX MX300HE		2016-10-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.900	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.201	50	99.9	0.072	0.077	0.029	26.2	7.2		69368

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.201	1.22	99.9		0.831	0.033	0.013	0.999	2.9	7.1

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5WSD	1.201	30	65837	3457	99.9	0.1489	0.1489	0.1786	0.1763	RANDOM	18.4495

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	0.701
s_from_restr_planes	0.408
s_approx_iso_adps	0.131
s_zero_chiral_vol	0.061
s_similar_adp_cmpnt	0.045
s_rigid_bond_adp_cmpnt	0.027
s_angle_d	0.024
s_bond_d	0.007
s_similar_dist
s_anti_bump_dis_restr

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1839
Nucleic Acid Atoms
Solvent Atoms	294
Heterogen Atoms	15

Software

Software
Software Name	Purpose
HKL-2000	data scaling
SHELX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing