1RMQ | pdb_00001rmq

Crystal structure of AphA class B acid phosphatase/phosphotransferase with osmiate mimicking the catalytic intermediate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1N8N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	293	AphA 6mg/mL, 50mM Na acetate, 25% PEG 6000, 10mM osmiate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.732	α = 90
b = 66.447	β = 121.3
c = 91.523	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	MARRESEARCH	Double crystal monochromator	2002-02-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	1.13980, 1.14057, 1.13800	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2	30.58	99.3	0.089	0.089	6.2	3.4	31710	31710			23.344

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.11	97.6		0.402	0.402	1.6	3.1	4531

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	1N8N	2	30	29421	29421	2265	99.25	0.18661	0.18661	0.18325	0.2019	0.23002	0.2435	RANDOM	26.179

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]
0.5		0.58	0.05		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	8.202
r_scangle_it	5.066
r_scbond_it	3.316
r_angle_refined_deg	1.943
r_mcangle_it	1.853
r_mcbond_it	1.135
r_metal_ion_refined	0.324
r_symmetry_vdw_refined	0.252
r_symmetry_hbond_refined	0.25
r_nbd_refined	0.222
r_xyhbond_nbd_refined	0.213
r_chiral_restr	0.148
r_bond_refined_d	0.026
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3282
Nucleic Acid Atoms
Solvent Atoms	296
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing