2W4P | pdb_00002w4p

Human common-type acylphosphatase variant, A99G

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		HUMAN COMMON-TYPE ACYPHOSPHATASE WILD TYPE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		2.4M SODIUM MALONATE, PH7.0 25% GLYCEROL

Crystal Properties
Matthews coefficient	Solvent content
1.85	33.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 24.206	α = 90
b = 57.339	β = 90
c = 58.777	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	287	IMAGE PLATE	RIGAKU IMAGE PLATE	MIRRORS	2006-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007

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	1.7	41	99.9	0.1	8.5	6.36		9498		2

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	1.7	1.74	98.4		0.24	2.1

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	HUMAN COMMON-TYPE ACYPHOSPHATASE WILD TYPE	1.7	41.03	9045	453	99.9	0.19	0.187	0.2	0.241	0.25	RANDOM	16.24

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]
-1.02			-1.14		2.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.096
r_dihedral_angle_3_deg	12.642
r_dihedral_angle_4_deg	9.829
r_dihedral_angle_1_deg	6.8
r_scangle_it	3.417
r_scbond_it	2.298
r_angle_refined_deg	1.55
r_mcangle_it	1.3
r_mcbond_it	1.097
r_angle_other_deg	0.848
r_mcbond_other	0.254
r_symmetry_vdw_other	0.227
r_symmetry_hbond_refined	0.22
r_nbd_other	0.197
r_nbd_refined	0.196
r_xyhbond_nbd_refined	0.193
r_nbtor_refined	0.177
r_symmetry_vdw_refined	0.11
r_chiral_restr	0.104
r_nbtor_other	0.085
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
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_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	768
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	6

Software

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