3RSM | pdb_00003rsm

Crystal structure of S108C mutant of PMM/PGM

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1K35	PDB ENTRY 1K35

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	1.4 Na,K tartrate, 100 mM Na Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.034	α = 90
b = 72.806	β = 90
c = 92.997	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			osmic confocal	2010-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.1	50.843	99.9	0.06	11	4.8	29797	29767

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18	99.9		0.5133	2.3	4.72

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	refinement	THROUGHOUT	PDB ENTRY 1K35	2.1	50.84	27273	1456	99.74	0.21463	0.21262	0.21	0.25252	0.25	RANDOM	54.927

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]
-1.55			0.21		1.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.309
r_dihedral_angle_4_deg	15.928
r_dihedral_angle_3_deg	15.719
r_dihedral_angle_1_deg	5.671
r_scangle_it	2.772
r_scbond_it	1.801
r_angle_refined_deg	1.387
r_mcangle_it	0.991
r_mcbond_it	0.54
r_chiral_restr	0.088
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3246
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms	6

Software

Software
Software Name	Purpose
CrystalClear	data collection
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling