9JNC | pdb_00009jnc

Crystal Structure of SME-1 with improved electron density

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DY6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	20% PEG 4000, 0.2M Lithium Chloride

Crystal Properties
Matthews coefficient	Solvent content
2.16	41.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.011	α = 90
b = 51.918	β = 113.25
c = 74.925	γ = 90

Symmetry
Space Group	P 1 21 1

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	RIGAKU HyPix-6000HE		2024-06-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.57	24.301	99.9	0.995	12.2	12.2		16226

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.57	2.68			0.854

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.57	24.301	16216	767	99.84	0.208	0.2048	0.2051	0.2803	0.2805	17.462

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]
1.235		-0.58	-0.885		0.108

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.425
r_dihedral_angle_6_deg	12.902
r_dihedral_angle_1_deg	7.129
r_dihedral_angle_2_deg	6.526
r_lrange_it	6.124
r_rigid_bond_restr	3.804
r_scangle_it	2.566
r_mcangle_it	2.269
r_angle_refined_deg	1.842
r_scbond_it	1.591
r_mcbond_it	1.365
r_symmetry_nbd_refined	0.326
r_nbtor_refined	0.304
r_symmetry_xyhbond_nbd_refined	0.28
r_nbd_refined	0.224
r_xyhbond_nbd_refined	0.197
r_chiral_restr	0.137
r_ncsr_local_group_1	0.048
r_bond_refined_d	0.007
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4116
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
MOLREP	phasing