2P4U | pdb_00002p4u

Crystal structure of acid phosphatase 1 (Acp1) from Mus musculus

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		294	10mM Sodium acetate, 70% MPD, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.716	α = 90
b = 168.539	β = 90.96
c = 42.721	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	CCD	MAR CCD 165 mm		2007-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

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	1.9	20	98.7	0.116	19.09	3.6	49330	48689		-3	26.5

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)
	1.9	1.97	98.4		0.72	1.7	3.5	4836

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 (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 1XWW	1.9	20	46931	46931	2372	99.18	0.187	0.184	0.1865	0.236	0.2377	RANDOM	31.705

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]
0.38		0.21	-1.03		0.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.885
r_dihedral_angle_4_deg	17.637
r_dihedral_angle_3_deg	14.86
r_dihedral_angle_1_deg	6.227
r_scangle_it	3.847
r_scbond_it	2.774
r_mcangle_it	2.001
r_angle_refined_deg	1.5
r_mcbond_it	1.176
r_nbtor_refined	0.304
r_symmetry_hbond_refined	0.25
r_nbd_refined	0.203
r_symmetry_vdw_refined	0.168
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.109
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4887
Nucleic Acid Atoms
Solvent Atoms	296
Heterogen Atoms	20

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection