1WAR | pdb_00001war

Recombinant Human Purple Acid Phosphatase expressed in Pichia Pastoris

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1			277	THE PROTEIN (10 MG/ML) IN 50 MM MES AT PH 6, WAS PASSED THROUGH AN ULTRAFREE-MC 0.22 MM SPIN FILTER UNIT (MILLIPORE) AND ALLOWED TO STAND AT 4 DEGREES C. PURPLE CRYSTALS GREW SPONTANEOUSLY OVERNIGHT AND REACHED SIZES UP TO 0.5 MM IN SEVERAL WEEKS.

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.538	α = 90
b = 80.538	β = 90
c = 99.998	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	300	IMAGE PLATE	MAR scanner 345 mm plate	OSMIC MIRRORS	2003-08-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

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	2.22	18.98	94.5	0.07	17.97	4.2		15951		-3	36

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	2.22	2.3	94		0.4	5.49	4.2

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1UTE	2.22	18.98	15167	767	94.7	0.141	0.138	0.16	0.198	0.21	RANDOM	32.02

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]
-0.78			-0.78		1.55

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	10.013
r_scbond_it	6.455
r_dihedral_angle_1_deg	6.366
r_mcangle_it	4.614
r_mcbond_it	2.645
r_angle_refined_deg	1.373
r_angle_other_deg	0.862
r_symmetry_vdw_other	0.254
r_nbd_other	0.236
r_nbd_refined	0.182
r_symmetry_hbond_refined	0.157
r_xyhbond_nbd_refined	0.149
r_nbtor_other	0.081
r_chiral_restr	0.077
r_symmetry_vdw_refined	0.059
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2477
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing