1UGU | pdb_00001ugu

Crystal structure of PYP E46Q mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PHY	PDB ENTRY 2PHY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	PEGMME 2000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.71	27.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.352	α = 90
b = 40.352	β = 90
c = 118.001	γ = 120

Symmetry
Space Group	P 65

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	MARRESEARCH		2003-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	0.650	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.2	35	94.5	0.037	18.1	8.3	33512	31902			14.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.2	1.24	82.4		0.368	3.4	5.6	3170

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	THROUGHOUT	PDB ENTRY 2PHY	1.2	34.92	31742	31742	1699		0.16658	0.16658	0.16523	0.17	0.19113	0.19	RANDOM	14.293

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]
0.49	0.25		0.49		-0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.941
r_scangle_it	3.243
r_sphericity_free	2.973
r_sphericity_bonded	2.835
r_scbond_it	2.141
r_mcangle_it	1.853
r_angle_refined_deg	1.44
r_mcbond_it	1.187
r_rigid_bond_restr	1.15
r_angle_other_deg	0.806
r_nbd_other	0.291
r_nbd_refined	0.287
r_symmetry_hbond_refined	0.25
r_xyhbond_nbd_refined	0.243
r_symmetry_vdw_other	0.212
r_symmetry_vdw_refined	0.156
r_nbtor_other	0.1
r_chiral_restr	0.098
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_gen_planes_other	0.008
r_bond_other_d
r_dihedral_angle_2_deg
r_xyhbond_nbd_other
r_symmetry_hbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	966
Nucleic Acid Atoms
Solvent Atoms	180
Heterogen Atoms	11

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing