1SY2 | pdb_00001sy2

1.0 A Crystal Structure of D129A/L130A Mutant of Nitrophorin 4

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1D2U	PDB entry 1D2U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	Ammonium Phosphate 2.8 M, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.149	α = 90
b = 42.804	β = 93.93
c = 52.881	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	ADSC QUANTUM 315	Flat mirror (vertical focusing)	2002-05-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.98	SSRL	BL11-1

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	0.99	21.4	98.8	0.049	0.049	27.3	4.62	85962	85962			6.62

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)
	0.99	1.03	99.4		0.157	0.157	7.7	3.34	8609

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	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 1D2U	1	21.4	85962	77984	4104	97.27	0.1563	0.1563	0.15559	0.16	0.1696	0.16	RANDOM	8.691

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]
-0.07		-0.03	0.05		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.532
r_sphericity_free	3.625
r_scangle_it	3.165
r_sphericity_bonded	2.915
r_scbond_it	2.155
r_mcangle_it	1.987
r_angle_refined_deg	1.66
r_mcbond_it	1.29
r_rigid_bond_restr	1.09
r_angle_other_deg	0.794
r_nbd_other	0.254
r_symmetry_vdw_other	0.219
r_nbd_refined	0.217
r_symmetry_vdw_refined	0.146
r_xyhbond_nbd_refined	0.117
r_nbtor_other	0.11
r_chiral_restr	0.098
r_symmetry_hbond_refined	0.058
r_bond_refined_d	0.012
r_metal_ion_refined	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002
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_other
r_symmetry_hbond_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1450
Nucleic Acid Atoms
Solvent Atoms	258
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
d*TREK	data scaling