7NB5 | pdb_00007nb5

Structure of EstD11 S144A in complex with naproxen p-nitrophenol ester

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7AT0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	291	Sodium formate 3.2M and citrate pH 5 0.1M

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.999	α = 90
b = 89.705	β = 90
c = 125.762	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2020-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	2.13	44.84	99.9	0.067	0.027	0.998	18.2	6.7		15581

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.13	2.19	100		0.231	0.09	0.989	8.2

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	7AT0	2.13	42.36	14812	768	99.74	0.17027	0.16738	0.18	0.22773	0.24	RANDOM	39.253

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]
-2.33			4.43		-2.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.465
r_dihedral_angle_4_deg	19.041
r_long_range_B_other	14.026
r_long_range_B_refined	13.991
r_dihedral_angle_3_deg	13.875
r_scangle_other	13.177
r_scbond_it	10.773
r_scbond_other	10.769
r_mcangle_other	7.515
r_mcangle_it	7.492
r_mcbond_other	6.265
r_mcbond_it	6.263
r_dihedral_angle_1_deg	5.2
r_angle_refined_deg	1.237
r_angle_other_deg	1.049
r_chiral_restr	0.074
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2247
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing